Computational Biochemistry Research Group

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  • ETH: Computational Biochemistry Research Group Home h
    Computational Biochemistry Research Grou Please visit this site often. ( This site last updated March 23, 2001 > This page last updated March 23, 2001 ">March 23, 2001 among a host of other services
    • Darwin 2.0 Available
      Computational Biochemistry Research Grou We announce the availability of the second release of Darwin v. 2.0 , an interpreted computer language especially tailored to researchers in the biosciences. D
    • CBRG News
      Computational Biochemistry Research Grou CBRG Home Services Darwin Research Students Search Contact Site Ma (This page last updated Saturday, Friday, August 3, 2000) DATE SUBJECT NEWS - LINKS 03.Au
      • ETH: CBRG
        Computational Biochemistry Research Grou Server News The server has been down since February 21st. Hopefully everything is back up and running now. Please let us know if some function is not working.
      • Darwin 2.0 Delayed
        Computational Biochemistry Research Grou Darwin 2.0 Delayed Darwin 2.0 has been delayed. If you have already submitted a Darwin 2.0 System Agreement, we will let you know as soon as your versions are
    • Services - ASAS: Alerting of Structurally Ambivalent Sequences
      Computational Biochemistry Research Grou The program Alerting of Structurally Ambivalent Sequences (ASAS) parses the submitted sequence, matching its subsequences (tetrapeptides to nonapeptides) again
    • CBRG Server Main Page - Services Offered
      Computational Biochemistry Research Grou (This page last updated Monday, May 21, 2001 ) Welcome to the CBRG server of ETHZ. All the queries submitted to the system are processed with the Darwin system
      • ETH: CBRG - Services - VertexCover
        Computational Biochemistry Research Grou A vertex cover of a graph is a set of vertices (nodes) which covers all the edges. A standard reference for this problem is ``Computers and Intractability'', [
      • CBRG - AllAllDB: Querying the all-against-all database of SwissProt
        Computational Biochemistry Research Grou Next: MassSearch: Searching SwissProt Up: Computational Biochemistry Research Previous: AllAll: Related peptide Filling and submitting the following form
        • Server Booklet - AllAllDB
          Computational Biochemistry Research Grou Next: Usage Up: The Computational Biochemistry Server Previous: Structure prediction according Usage Examples Restrictions and common problems Related D
          • Server Booklet - AllAllDB: Restrictions and common problems
            Computational Biochemistry Research Grou Next: Related Darwin functions Up: AllAllDB: querying the Previous: Examples Restrictions and common problems The number of matches being reported in a si
          • Structure prediction according the E.T.H. method
            Next: AllAllDB: querying the Up: Methods and applications Previous: Multiple alignment and The E.T.H. method [4][7][3] for predicting the conformation of proteins extracts information from patter
          • Server Booklet - References
            Computational Biochemistry Research Grou Up: The Computational Biochemistry Server Previous: Peptide gap penalties References Hans-Jürgen Bandelt and Andreas W.M. Dress. Split decomposition: a new
            • Server Booklet - Peptide gap penalties
              Computational Biochemistry Research Grou Next: References Up: The Computational Biochemistry Server Previous: Amino acid similarity The gap penalty being used for a gap of amino acids at pam is [
          • Server Booklet - AllAllDB: Usage
            Computational Biochemistry Research Grou Next: Examples Up: AllAllDB: querying the Previous: AllAllDB: querying the To select the matches, the following criteria can be used: OneID: a list of ID
          • Server Booklet - AllAllDB: Related Darwin functions
            Computational Biochemistry Research Grou CBRG Home Services Darwin Research Students Search Contact Site Ma Next: Methods Up: AllAllDB: querying the Previous: Restrictions and common Related Da
          • Contents
            Next: PepPepSearch: searching SwissProt Up: The Computational Biochemistry Server Previous: The Computational Biochemistry Server Contents Contents PepPepSearch: searching SwissProt for a peptide
            • Server Booklet - Amino Acids
              Computational Biochemistry Research Grou Next: Bases Up: The Computational Biochemistry Server Previous: Amino acidsbases, The following table contains the amino acids, their abbreviations and the
            • Server Booklet - Amino acid similarity matrix at 250 PAM
              Computational Biochemistry Research Grou Next: Peptide gap penalties Up: The Computational Biochemistry Server Previous: Genetic code To compute the final score, once that we have obtained an esti
            • Server Booklet - Genetic Code
              Computational Biochemistry Research Grou Next: Amino acid similarity Up: The Computational Biochemistry Server Previous: Bases Codons containing an X are translated into an amino acid if the tran
            • Server Booklet - Amino acids, bases, and similarity scores
              Computational Biochemistry Research Grou CBRG Home Services Darwin Research Students Search Contact Site Ma Next: Amino acids Up: The Computational Biochemistry Server Previous: Methods Amino ac
            • Server Booklet - Bases
              Computational Biochemistry Research Grou Next: Genetic code Up: The Computational Biochemistry Server Previous: Amino acids Bases The following table contains the bases and their abbreviations. No
          • Server Booklet - AllAllDB: Methods
            Computational Biochemistry Research Grou Next: MassSearch: searching SwissProt Up: AllAllDB: querying the Previous: Related Darwin functions Matches are stored in a grid file [21], a data struct
        • Server Booklet - AllAllDB: Examples
          Computational Biochemistry Research Grou CBRG Home Services Darwin Research Students Search Contact Site Ma Next: Restrictions and common Up: AllAllDB: querying the Previous: Usage Examples Su
        • ETH: CBRG - AllAll Related Peptide Sequence Search
          Computational Biochemistry Research Grou AllAll: Related peptide sequences Filling and submitting the following form (see also the example) will start an all against all of the given sequences and com
      • CBRG eMail Server
        Computational Biochemistry Research Grou Next: Accessing the CBRG Accessing the CBRG server by e-mail AllAll: Related peptide sequences AllAllDB: Querying the all-against-all database of SwissProt U
      • Services - FastaToDarwin: Convert Fasta Sequences to Darwin Format
        Computational Biochemistry Research Grou Up: Computational Biochemistry Research Previous: VertexCover Paste your FASTA sequences in the window below and FastaToDarwin will convert your sequences t
        • Services - FastaToDarwin: Example
          Computational Biochemistry Research Grou FastaToDarwin: Convert FASTA sequences to Darwin format Paste your FASTA sequences in the window below and FastaToDarwin will convert your sequences to Darwin
      • CBRG - PredictGenes: Predict and verify gene structure by alignment with homologous proteins
        Computational Biochemistry Research Grou Next: MultiAlign Up: Computational Biochemistry Research Previous: darwin: Run a Filling and submitting the following form (see also the example) will pred
        • Server Booklet - PredictGenes: predict and verify gene structure by alignment with homologous proteins
          Computational Biochemistry Research Grou Next: Usage Up: The Computational Biochemistry Server Previous: Restrictions and common The output of PredictGenes is similar to an EMBL database entry. Pr
          • Methods
            Next: Amino acidsbases, Up: PredictGenes: predict and Previous: Related Darwin functions Methods The methods used for PredictGenes are basically identical to the methods in Sect. 5.5. CBRG
          • Usage
            Next: Examples Up: PredictGenes: predict and Previous: PredictGenes: predict and The sequence identification is copied into the output. The other options request a graphical visualization of all
          • Restrictions and common problems
            Next: PredictGenes: predict and Up: Darwin: running the Previous: Examples Operations that write files or read arbitrary files cannot be executed by the server: !, AddGF, appendto, CompressGF, C
          • Restrictions and common problems
            Next: Related Darwin functions Up: PredictGenes: predict and Previous: Examples Restrictions and common problems If no significant matches are found, only the raw prediction is output (if selecte
          • Related Darwin functions
            Next: Methods Up: PredictGenes: predict and Previous: Restrictions and common Related Darwin functions LoadFile, DMDMS, NPBestPamShake, NPMatch, NPOneAllMatch, print, Intron, PredictGenes. CBRG
        • CBRG - DARWIN: Run a DARWIN program
          Computational Biochemistry Research Grou Next: PredictGenes: predict and Up: Computational Biochemistry Research Previous: TreeGen: Tree generation Filling and submitting the following form (see
        • PredictGenes Example
          Next: Restrictions and common Up: PredictGenes: predict and Previous: Usage Submitting the following form produces several pages of results. The result should be mailed to: Sequence ID: Target
      • Services - Run a Darwin program
        Computational Biochemistry Research Grou Next: PredictGenes: predict and Up: Computational Biochemistry Research Previous: TreeGen: Tree generation Filling and submitting the following form (see
        • Server Booklet - Darwin: Running the Darwin Tool
          Computational Biochemistry Research Grou Next: Usage Up: The Computational Biochemistry Server Previous: Methods The Darwin command runs a complete Darwin program [15]. Usage Examples Restrictio
          • Usage
            Next: Examples Up: Darwin: running the Previous: Darwin: running the The darwin program has to be any sequence of Darwin statements forming a program. Besides the Darwin language and its standard
          • Methods
            Next: Darwin: running the Up: TreeGen: tree generation Previous: Related Darwin functions Methods For tree construction methods, see AllAll methods. For split decomposition, see [1]. CBRG
        • Server Booklet - Darwin: A Fun Example
          Computational Biochemistry Research Grou Next: Restrictions and common Up: Darwin: running the Previous: Usage The following program searches the SwissProt database for your name and lists the p
        • Examples
          Next: Restrictions and common Up: Darwin: running the Previous: Usage Submitting the following form produces several pages of results. Program: # Assign a nucleotide sequence to variable nuc nu
      • The Computational Biochemistry Server at ETHZ
        Next: Contents Gaston H. Contents PepPepSearch: searching SwissProt for a peptide sequence Usage Examples Restrictions and common problems Related Darwin functions Methods Finding candidates PAM
      • Services - MultiAlign: Multiple Sequence Alignment Tools
        Computational Biochemistry Research Grou Next: MassDynSearch Up: Computational Biochemistry Research Previous: Predict Genes Seperate your sequences and labels either with ';' or ':'. LabelsMultipl
      • CBRG - NuclPepSearch: Searching SwissProt for a nucleotide sequence
        Computational Biochemistry Research Grou Next: PepPepSearch: Searching SwissProt Up: Computational Biochemistry Research Previous: MassSearch: Searching SwissProt The result should be mailed to:
        • Server Booklet - NuclPepSearch
          Computational Biochemistry Research Grou Usage Examples Restrictions and common problems Related Darwin functions Methods Finding candidates Nucleotide peptide alignment PAM estimation and final
          • Server Booklet - NuclPepSearch: Restrictions and common problems
            Computational Biochemistry Research Grou Next: Related Darwin functions Up: NuclPepSearch: searching SwissProt Previous: Examples The number of complete alignments being printed and visualized is
          • Finding candidates
            Next: Nucleotide peptide alignment Up: Methods Previous: Methods The similarity score threshold for a refined alignment to be selected is In order to find candidates, every database sequence is a
          • Server Booklet - MassSearch Methods
            Computational Biochemistry Research Grou Next: NuclPepSearch: searching SwissProt Up: MassSearch: searching SwissProt Previous: Related Darwin functions For a complete description of the algorit
          • Server Booklet - NuclPepSearch: Related Darwin functions
            Computational Biochemistry Research Grou Next: Methods Up: NuclPepSearch: searching SwissProt Previous: Restrictions and common LoadFile, DMDMS, NPBestPamShake, NPMatch, NPOneAllMatch, print, Int
          • Nucleotide peptide alignment
            Next: PAM estimation and Up: Methods Previous: Finding candidates All candidate proteins from the exhaustive search with the hypothetical peptides are being compared directly to the nucleotide se
          • Methods
            Next: Finding candidates Up: NuclPepSearch: searching SwissProt Previous: Related Darwin functions Methods Finding candidates Nucleotide peptide alignment PAM estimation and final selection CBR
          • PAM estimation and final selection
            Next: TreeGen: tree generation Up: Methods Previous: Nucleotide peptide alignment For each candidate reaching the above goal, PAM distance and PAM variance are estimated. Finally, all sequences r
          • Usage
            Next: Examples Up: NuclPepSearch: searching SwissProt Previous: NuclPepSearch: searching SwissProt The output contains the SwissProt ID, the similarity score and the PAM distance for all sequence
        • CBRG - PepPepSearch: Searching SwissProt for a peptide sequence
          Computational Biochemistry Research Grou Next: TreeGen: Tree generation Up: Computational Biochemistry Research Previous: NuclPepSearch: Searching SwissProt Filling and submitting the following
        • Server Booklet - NuclPepSearch: Examples
          Computational Biochemistry Research Grou Next: Restrictions and common Up: NuclPepSearch: searching SwissProt Previous: Usage Submitting the following form produces several pages of results. The
      • Services - MassDynSearch: Searching SwissProt by protein mass after C or N-terminal gestion
        Computational Biochemistry Research Grou Searching SwissProt by protein mass after C or N-terminal digestion For problems, questions or suggestions feel free to send a mail to darwin.comments@inf.ethz.ch CBRG {w
        • Server Booklet - MassDynSearch
          Computational Biochemistry Research Grou Filling and submitting the following form (see also the example) will search the SwissProt database for sequences. Enter the sequence of masses for each fragment
      • Services - AllAll (Alignment, MSA, Probable Ancestral Sequence)
        Computational Biochemistry Research Grou Filling and submitting the following form (see also the example) will start an all against all of the given sequences and compute various derived results. Desi
        • Server Booklet - AllAll: Examples
          Computational Biochemistry Research Grou Next: Restrictions and common Up: AllAll: Related peptide Previous: Commands Examples Submitting the following form produces several pages of results. Th
          • Server Booklet - AllAll: Restrictions and common problems
            Computational Biochemistry Research Grou Next: Related Darwin functions Up: AllAll: Related peptide Previous: Examples If the similarity between two sequences is less then 80, PAM distance is set
          • Commands
            Next: Examples Up: Usage Previous: Sequence specification The following commands are available: The command PamData returns the estimated pam distances and variances between each pair of sequences
        • Server Booklet - AllAll
          Computational Biochemistry Research Grou Usage Sequence specification Commands Examples Restrictions and common problems Related Darwin functions Methods and applications Tree construction Mult
          • PAM estimation and final selection
            Next: AllAll: Related peptide Up: Methods Previous: Finding candidates For each candidate reaching the goal, PAM distance and PAM variance are estimated. For the PAM variance, we need the second
          • Tree construction
            Next: Multiple alignment and Up: Methods and applications Previous: Methods and applications For an introduction to the subject, see [14]. Given PAM distances and their variances for each pair
          • Multiple alignment and probabilistic ancestral sequence
            Next: Structure prediction according Up: Methods and applications Previous: Tree construction The multiple alignment and probabilistic ancestral sequence (PAS) are computed simultaneously. The si
          • Server Booklet - AllAll: Related Darwin functions
            Computational Biochemistry Research Grou Next: Methods and applications Up: AllAll: Related peptide Previous: Restrictions and common BestPamShake, DMDMS, DrawSplits, DrawTree, dSplits, KWIndex,
          • Server Booklet - AllAll: Methods and applications
            Computational Biochemistry Research Grou Next: Tree construction Up: AllAll: Related peptide Previous: Related Darwin functions Tree construction Multiple alignment and probabilistic ancestral s
          • Server Booklet - AllAll Usage
            Computational Biochemistry Research Grou CBRG Home Services Darwin Research Students Search Contact Site Ma Next: Sequence specification Up: AllAll: Related peptide Previous: AllAll: Related pe
        • ETH: CBRG
          Computational Biochemistry Research Grou To specify the related peptide sequences (at least three!), you can use four different formats that may be freely mixed in a request: The sequence is given exp
        • Services - AllAll - FAQ
          Computational Biochemistry Research Grou back to AllAll AllAll FAQ No matter what I do, I receive an error message when I submit jobs that says, "Your AllAll request does not request any command. If y
      • Services - PepPepSearch: Searching SwissProt for a peptide sequence
        Computational Biochemistry Research Grou Next: TreeGen: Tree generation Up: Computational Biochemistry Research Previous: NuclPepSearch: Searching SwissProt Filling and submitting the following
        • Server Booklet - PepPepSearch: Examples
          Computational Biochemistry Research Grou Next: Restrictions and common Up: PepPepSearch: searching SwissProt Previous: Usage Submitting the following form produces several pages of results. The
        • Server Booklet - PepPepSearch
          Computational Biochemistry Research Grou Next: Usage Up: The Computational Biochemistry Server Previous: Contents Usage Examples Restrictions and common problems Related Darwin functions Method
          • Server Booklet - Related Darwin functions
            Computational Biochemistry Research Grou Next: Methods Up: PepPepSearch: searching SwissProt Previous: Restrictions and common BestPamShake, DMDMS, LoadFile, Match, OneAllMatch, print, RefineShak
          • Server Booklet - PepPep Methods
            Computational Biochemistry Research Grou Next: Finding candidates Up: PepPepSearch: searching SwissProt Previous: Related Darwin functions A score of 120 therefore means that it is times more li
          • Finding candidates
            Next: PAM estimation and Up: Methods Previous: Methods In order to find candidates, every database sequence is aligned with the target sequence using a 250 PAM similarity matrix (see appendix A.
      • CBRG - TreeGen: Tree generation from distance data
        Computational Biochemistry Research Grou The result should be mailed to: Distance matrix (symmetric, rows separated by ';', 0 marks element i,i): Variance matrix (optional, format like distance matr
        • Examples
          Next: Related Darwin functions Up: TreeGen: tree generation Previous: Usage Submitting the following form produces several pages of results. The result should be mailed to: Distance matrix (symm
          • Related Darwin functions
            Next: Methods Up: TreeGen: tree generation Previous: Examples Related Darwin functions DrawSplits, DrawTree, dSplits, MinSqTree, NBody. CBRG
          • Usage
            Next: Examples Up: TreeGen: tree generation Previous: TreeGen: tree generation The distance and variance matrices contain one row for each node. Optionally, variances for these distance estimates
        • Server Booklet - TreeGen
          Computational Biochemistry Research Grou Next: Usage Up: The Computational Biochemistry Server Previous: PAM estimation and The TreeGen command calculates phylogenetic trees, split graphs and 2D p
        • ETH: CBRG - TreeGen FAQ
          Computational Biochemistry Research Grou TreeGen FAQ In my AllAll job, I asked for an unrooted tree. Where is it? If your question has not been answered in the above FAQ, please ask it by emailing dar
      • Services - MassSearch: Searching SwissProt or EMBL by protein mass after digestion
        Computational Biochemistry Research Grou Next: NuclPepSearch: Searching SwissProt Up: Computational Biochemistry Research Previous: AllAllDB: Querying the You can chose between monoisotopic and averag
    • CBRG - Research
      Computational Biochemistry Research Grou (This page last updated Friday, May 17, 2001 ) Xianghong Zhou projects include: Have some fun with our new Applets: ETH CBRG HomeBioOperaInstitue for Scientifi
      • Faces
        Bitte warten Sie einem Moment... Das Applet soll helfen folgende Fragen zu beantworten: Sie sind Besucher Nummer  F¸r Vorschl”ge und Fragen bitte schicken Sie eine Email an korosten@inf.ethz.ch , oder
      • plants
        Please wait a moment... This applet should help to answer the following questions: You are visitor number  For suggestions and questions feel free to send a mail to korosten@inf.ethz.ch , or visit my
      • Faces
        Bitte warten Sie einem Moment... Das Applet soll helfen folgende Fragen zu beantworten: Sie sind Besucher Nummer  F¸r Vorschl”ge und Fragen bitte schicken Sie eine Email an korosten@inf.ethz.ch , oder
      • plants
        Please wait a moment... This applet should help to answer the following questions: You are visitor number  For suggestions and questions feel free to send a mail to korosten@inf.ethz.ch , or visit my
      • Faces
        Evolution of Comic Faces Purpose of the applet: List of the commands: You are visitor number  For suggestions and questions feel free to send a mail to korosten@inf.ethz.ch , or visit my homepage: Cha
      • Faces
        Please wait a moment... This applet should help to answer the following questions: You are visitor number  For suggestions and questions feel free to send a mail to korosten@inf.ethz.ch , or visit my
    • CBRG - Publications
      Computational Biochemistry Research Grou CBRG Home Services Darwin Research Students Search Contact Site Ma Selected Publications Steven A. Benner. Predicting de novo the folded structure of protein
    • DARWIN's Homepage
      Computational Biochemistry Research Grou In an effort to connect Darwin users together, we have started a Darwin Listserver here at the ETH. (This page last updated May 17, 2001 ) Enter you email addr
      • A tutorial introduction to Computational Biochemistry using Darwin
        Contents Interaction with the Darwin system Writing functions Handling text Arrays and lists Input/output Advanced programming Dayhoff matrices and mutation matricesGap probabilities and gap penalties
        • Comparing sequences
          The sequences in a match are defined by offsets into the database and their corresponding lengths. SprintMatch  is also a low level function which takes a match and a similarity matrix and returns a t
        • Evolution phylogenetic trees
          Since we do not have information about the internal nodes, all our computations will be based on the external nodes (present day) information. An ept will be one which reflects the distance constraint
        • Writing functions
          A procedure can consist of a one or many statements.  Multiple statements will be needed when the computation of the function requires various steps. The procedures that we have written so far are rat
        • Quick Darwin
          Next: Families of sequences in A tutorial introduction to Previous: Families of sequences in Quick Darwin A short reference of the users-oriented functions in Darwin. Marcel TURCOTTE Thu Oct 31 08:31
        • Finding close-to-identical entries
          Next: Building a phylogenetic tree Up: A tutorial introduction to Previous: Reformatting a database to Finding close-to-identical entries To be written ignore off Marcel TURCOTTE Thu Oct 31 08:31:39
        • Computing expected scores
          The two bounds, Error, cannot convert to a number are not very close for this example. Given these bounds on the similarity we are now able to run the search. Marcel TURCOTTE Thu Oct 31 08:31:39 EST
        • All-against-all matching
          Next: Previous: Comparing sequences All-against-all matching a chapter on SelfMatch, how to handle large volumes of output and SmallAllAll To be written ignore off Marcel TURCOTTE Thu Oct 31 08:31:39
        • Generating several ept topologies
          The function PhyloTree will print a message every time that it finds a merging order which is less than 95% probable. ignore off Next: Probabilistic ancestral sequences and Up: Building a phyloge
        • Handling text
          Next: Arrays and lists Up: A tutorial introduction to Previous: Writing functions Handling text Text, names, offsetting, selection, concatenation, text searching. To be written Marcel TURCOTTE Thu Oc
        • Families of sequences in a database
          To construct the families we need the set of all significant matches between a group of sequences, or in our terminology, an all-against-all matching. The results of this function are produced in two
        • Visualization of data
          A simple example is a plot of for : > plot(x->sin(x),-5..5); After this command, Darwin has created a PostScript file that can be printed by the command !lpr temp.ps, producing the plot in figure .
        • Random amino acid sequences
          We would like to perform mutations on this sequence, equivalent to a given evolutionary distance.  Since we will want to perform more than one random experiment, it is appropriate to write a function
        • Probabilistic ancestral sequences and multiple alignments
          It is a natural concept to define a probabilistic amino acid sequence. Describing the amount of information of each probabilistic position. Describing sequences as probabilistic sequences is a tool wh
        • Arrays and lists
          Previous: Handling text Arrays and lists Lists, vectors, arrays, matrices, selection, MatrixToRow, NewArray, Search arrays, sort, printing arrays. To be written Marcel TURCOTTE Thu Oct 31 08:31:39 ES
        • Quick Darwin
          Next: About this document Up: A tutorial introduction to Previous: Families of sequences in Quick Darwin A short reference of the users-oriented functions in Darwin. Marcel TURCOTTE Thu Oct 31 08:31:
        • Gap probabilities and gap penalties
          The purpose of aligning sequences with dynamic programming is to find the alignment which maximizes the probability of the two sequences having evolved  from a common ancestor as opposed to being just
        • Contents
          Darwin (Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences) is an interactive system for doing sequence matching and sequence analysis. This tutorial is organized in a very loose wa
          • Sample Session
            This is a quick introduction to Darwin (Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences) through a sample session. Now compute a subset of the all-against-all   matching of the e
        • Order k stochastic sequences
          Random amino acid sequences Order k stochastic sequences The random sequences generated with RandomSeq follow exclusively the individual probabilities of the amino acids. ignore off Marcel TURCOTTE T
        • A model of insertions/deletions
          Next: The GKSKGFGFV sequence Up: A tutorial introduction to Previous: Probabilistic ancestral sequences and A model of insertions/deletions To be written ignore off Marcel TURCOTTE Thu Oct 31 08:31:3
        • Input/output
          Next: Advanced programming Up: A tutorial introduction to Previous: Arrays and lists Input/output I/O, lprint, print, printf, readfile. To be written Marcel TURCOTTE Thu Oct 31 08:31:39 EST 1996
        • About this document ...
          This document was generated using the LaTeX2HTML translator Version 96.1 (Feb 5, 1996) Copyright © 1993, 1994, 1995, 1996, Nikos Drakos, Computer Based Learning Unit, University of Leeds. The command
        • Computation of matrices
          Every time that we use the Dayhoff function, Darwin also assigns the natural logarithm  of the corresponding mutation matrix M to the global variable logPAM1.  From the previous computations, the firs
        • Building a phylogenetic tree from the results of an all-against-all matching
          A phylogenetic tree is a representation of the evolution of species . In this chapter we will assume that we do not have any additional biological information about the phylogeny; i.e. we will derive
        • Computing estimates of PAM distances between species
          In this section we will select a few species, easily identifiable even to the layman in the area, and compute an estimate of their PAM distance.  This distance between a pair of species, assuming that
        • The GKSKGFGFV sequence
          One of the services that computational biochemistry provides is the searching of databases based on small sequence fragments. The function OneAllMatch  can be used to compare a given sequence with an
        • Advanced programming
          Advanced programming Data structures, type testing, type definition, errors, traperror, other debugging tools, printlevel, option trace. To be written ignore off Marcel TURCOTTE Thu Oct 31 08:31:39 E
        • Estimating mutation matrices
          It is easy to see that the expected value of C is given by N is a diagonal matrix  where is the number of amino acids i in . The matrix N is obtained from counting all the amino acids analysed, and
        • Approximate topology of the tree
          and similarly for any i: We have now reduced the problem by one, and obtained a new distance matrix: For the next step the minimum distance is between 4 and 5 with a value of 7.2. where we call the ``
        • Interaction with the Darwin system
          Repetition  statements are called for  loops, they will execute an inner statement several times for different values of the loop variable, for example: > for i to 5 do i, i^2, i^3, log(i) od; 1, 1,
        • Families of sequences in a database
          To construct the families we need the set of all significant matches between a group of sequences, or in our terminology, an all-against-all matching. The results of this function are produced in two
        • Reformatting a database to conform the Darwin tagging conventions
          For the above sequence, we use three additional tags.  The DE tag, will normally contain the description of the sequence in question, the AU tag will name the person who provided the sequence and the
        • Generating random scores
          The following statements produce the random test sequences, match them to the given fragment, and update the statistical information using the updatew  function for both a refined match against a typi
        • Dayhoff matrices and mutation matrices
          A mutation matrix,  denoted by M, describes the probabilities of amino acid mutations for a given period of evolution. This corresponds to a model of evolution in which amino acids mutate randomly  an
      • What does DARWIN offer you?
        Computational Biochemistry Research Grou Next: What does Darwin Up: Darwina Computational Previous: What is Darwin A single, integrated tool for practical and experimental computational biochemi
      • How to obtain the DARWIN system
        Computational Biochemistry Research Grou   Next: Selected Publications Up: Darwina Computational Previous: How does working (This page last updated: Tuesday, November 9, 1999) The Darwin System
        • ETH: CBRG - Darwin License Agreement
          The Darwin System is an interactive and programmable system suitable for doing DNA/Peptide sequence matching and analysis. The system and its documentation are presently distributed in source/object f
        • Selected Publications of the CBRG
          Next: News (last update: Up: Computational Biochemistry Research Group Previous: How can you Selected Publications Steven A. Predicting de novo the folded structure of proteins. Current Opinion in
      • How to obtain Darwin
        Computational Biochemistry Research Grou Selected Publications Up: Darwina Computational Previous: How does working How to Obtain The Darwin System (This page last updated: October 23, 2000) The Darwi
      • What does DARWIN require?
        Computational Biochemistry Research Grou Next: How does working Up: Darwina Computational Previous: What does Darwin What does DARWIN require ? A UNIX based workstation. Currently there are impl
      • Functions in Darwin that are better than other systems
        Computational Biochemistry Research Grou Back to Darwin's Home Functions in Darwin that we think are better than the ones provided by other systems: Local Alignments at Best PAM. This is a simple alig
      • What is DARWIN?
        Computational Biochemistry Research Grou Next: What does Darwin Up: Darwina Computational Previous: Darwina Computational An acronym: Darwin stands for Data Analysis and Retrieval With Indexed N
      • What does working with DARWIN look like?
        Computational Biochemistry Research Grou We start by loading release 25 of the SwissProt database: > LoadFile (SwissProt25); Reading 19826007 characters from file SwissProt25 Pre-processing input (p
    • Search the CBRG and find links to other sites
      Computational Biochemistry Research Grou Your one stop shopping page for Compuatational Biochemistry links. Try Ari's Bioinformatics Web Log too Databases Interesting SARC - Virus Hoaxes If you have s
      • Ari's Bioinformatics Weblog
        Computational Biochemistry Research Grou DNA microarrays are reshaping basic biology--but scientists fear they may soon drown in the data Comparative Evolutionary Analysis of Mitochondrial Genomes Usi
    • CBRG Contact Information
      Computational Biochemistry Research Grou Institute for Scientific Computing/CBRG Switchboard: +41 1 632 74 71 Telefax: +41 1 632 13 74 Postal Address: Institut für Wissenschaftliches Rechnen
    • Diplomarbeits and Semesterarbeits Offered by The CBRG
      Computational Biochemistry Research Grou CBRG Home Services Darwin Research Students Search Contact Site Ma Diplomarbeits and Semesterarbeits offered by the CBRG. Interested? Please contact Mike Hal
    • AllAll Cross-Comparisons of Swiss-Prot38
      Computational Biochemistry Research Grou News:  Swiss-Prot version 38 has been completed and will be made available shortly. A new darwin database file and cross comparison will be returned to you by
    • CBRG Server Statistics
      Computational Biochemistry Research Grou CBRG Home Services Darwin Research Students Search Contact Site Ma CBRG Server Statistics Average/Year Non-ETHZ Back to Server Back to CBRG Home Comments, qu
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