Sequence Alignment & Analysis

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1. Pre-Sequence Analysis
2. Sequence Database Search
3.
   a.
   b.
Sequence Alignment
  •     Pairwise
  •     Multiple Alignment
  • 4. Patterns,  Motifs & Profiles
    5. Phylogenetic Analysis
    6. Secondary Structure Prediction
    7. Hydrophobicity/ Hydrophilicity
    8. Nucleic Acid Analysis
    9. Gene Finding
    10. RNA Analysis
    11. Primer Selection
    12. Integrated Sequence Analysis

    1. Pre-Sequence Analysis

    ISOELECTRIC   :as part of GCG package only.
    Isoelectric plots the charge as a function of pH for any peptide sequence.

     
    PEPTIDEMAP   :as part of GCG package only.
    PeptideMap creates a peptide map of an amino acid sequence.

     
    -MELTSIM :-
    Statistical mechanical simulation of polymeric DNA melting.

     
    *3*TagIdent tool (formerly GuessProt) :-
    Compares the pI and Mw combination of your unknown protein against
    a library of calculated Mw & pI's  for known proteins in SWISSPROT
    at ExPASy, Switzerland

     
    *2*PROPSEARCH :-
    Protein Sequence Search for Structural Homology
    Compares the relative amino acid composition of your unknown protein
    against a database of compositions calculated for all SWISSPROT entries
    at EMBL-Heidelberg

     
    PEPTIDESEARCH:-
    Makes a comparison between the molecular and peptide masses (of the segments
    generated by partial chemical or enzymatic digestion) of your unknown protein
    against a database of peptide fragment maps calculated (or empirically
    determined) for known proteins.

     
    MPCT :-
    Calculates (theoretical) the molecular mass, Isoelectric point & amino acid
    characteristics of your protein using only the sequence.

     
    PEPTIDEMASS :-
    Generates a theoretical peptide fragment map of your protein using only
    the sequence

     
    pI/Mw :-
    Compute the Theoretical pI and Molecular Weight of a Protein Sequence
    at ExPASy, Switzerland

     
    PROTEIN IDENTIFICATION  :-

     
    COMPUTATIONAL ANALYSIS :-


    2. Sequence Database Search

    BLAST :- 
    BLAST searches for sequences similar to a query sequence.  The query 
    and the database searched can be either peptide or nucleic acid in any
    combination. BLAST can search databases on your own computer or 
    databases maintained at the National Center for Biotechnology Information
    (NCBI) in Bethesda, Maryland, USA. 
    See also: 
    http://www.ncbi.nlm.nih.gov/BLAST/
    BLAST at GenomeNet, Japan,
    BLAST (with Entrez and SRS Links) at Baylor College of Medicine 

     
    FASTA:-
    FastA does a Pearson and Lipman search for similarity between a query 
    sequence and a group of sequences of the same type (nucleic acid or protein). 
    See also: 
    http://www2.ebi.ac.uk/fasta3/

     
    SCANPS :-
    Scan Protein Sequences at EBI , UK

     
    -The domain-server :-
    Direct prediction of protein domain-homologies from BLAST search

     
    PepPepSearch :-
    Search SwissProt for a Peptide Sequence at ETH-Zürich, Switzerland

     
    *2*PROPSEARCH :-
    Protein Sequence Search for Structural Homology
    Compares the relative amino acid composition of your unknown protein
    against a database of compositions calculated for all SWISSPROT entries
    at EMBL-Heidelberg

     
    -Family Pairwise Search :-
    With embedded motif models

     
    -WebBLAST 2.0 :-
    An integrated solution for organizing and analyzing sequence data.

     
    *2*Blocks+ :-
    A non-redundant database of protein alignment blocks derived
    from multiple compilation.

     
    EDITtoTREMBL :-
    A distributed approach to high-quality automated protein
    sequence annotation.

     
    -A novel method for automatic functional annotation
    of proteins

     
    KIND (Karolinska Institutet Nonredundant Database) :-
    A non-redundant protein database

     
    *2*WWW access to the SYSTERS
    protein sequence cluster set

     
    -ParAlign and SWMMX :-
    a parallel sequence alignment algorithm for
    rapid and sensitive database searches.

     
    -SAM-T98  (Sequence Alignment and Modeling) :-
    Hidden Markov models for detecting remote protein homologies.


    3. Sequence Alignments

    a. Pairwise Alignment

    GAP  :  as part of GCG package only.
    Gap uses the algorithm of Needleman and Wunsh to find the alignment 
    of two complete sequences that maximizes the number of matches and 
    minimizes the number of gaps.

     
    BESTFIT  :as part of GCG package only.
    BestFit makes an optimal alignment of the best segment of similarity 
    between two sequences.  Optimal alignments are found by inserting 
    gaps to maximize the number of matches using the local homology 
    algorithm of Smith and waterman.

     
    COMPARE  :as part of GCG package only.
    Compare compares two protein or nucleic acid sequences and creates a
    file of the points of similarity between them for plotting with DotPlot.
    Compare finds the points using either a window/stringency or a word
    match criterion. The word comparison is 1,000 times faster than the 
    window/stringency comparison, but somewhat less sensitive.

     
    DOTPLOT  :as part of GCG package only.
    DotPlot makes a dot-plot with the output file from Compare, FoldRNA,
    or StemLoop.

     
    PLOTSIMILARITY  :as part of GCG package only.
    PlotSimilarity plots the running average of the similarity among the 
    sequences in a multiple sequence alignment.

     
    FINDPATTERNS :as part of GCG package only.
    FindPatterns identifies sequences that contain short patterns like
    GAATTC or YRYRYRYR. You can define the patterns ambiguously 
    and allow mismatches. You can provide the patterns in a file or 
    simply type them in from the terminal. 

     
    ALIGN:-
    Optimal Global Alignment of Two Sequences with No Short-cuts
    See also : 
    http://www.biochem.ucl.ac.uk/bsm/dbbrowser/ALIGN/ALIGN.html
    and Align at MIPS, Germany 

     
    Calign :-
    Aligning sequences with restricted affine gap penalties.
    Runs on Sun workstations running SunOS Unix.
    Available free of charge by anonymous ftp at
    ftp://iubio.bio.indiana.edu
    directory: molbio/align,
    files: calign.driver.c, calign.c

     
    Dotlet :-
    Diagonal plots in a Web browser

     
    *2*SSEARCH :-
    Universal Sequence Comparison Using the Smith-Waterman Algorithm
    at DDBJ, Japan

     
    SSP :-
    Nearest neighbour segment method for a single sequence by
    Solovyev and Salamov, USA

     
    -SAPS:-
    Statistical Analysis of Protein Sequences at ISREC, Switzerland


    b. Multiple Alignment

    PILEUP  :as part of GCG package only.
    PileUp creates a multiple sequence alignment from a group of related
    sequences using progressive, pairwise alignments.  It can also plot a 
    tree showing clustering relationships used to create the alignment.

     
    SEQLAB  :as part of GCG package only.
    SeqLab is the graphical user interface to the Wisconsin Package.
    It is an interactive multiple sequence analysis tool that lets you view
    and refine alignments both by hand and by calling Wisconsin Package
    programs like PileUp.  You can do any analysis available in the 
    Wisconsin Package from SeqLab.

     
    CONSENSUS   :as part of GCG package only.
    Consensus calculates a consensus sequence for a set of pre-aligned short
    nucleic acid sequences by tabulating the percent of G, A, T, and C for each
    position in the set. FitConsensus uses the Consensus output table as a probe
    to search for the best examples of the derived consensus in other nucleotide 
    sequences.

     
    AMAS :-
    Analysis of a multiply aligned set of sequences by
    Livingstone & Barton, Oxford, UK
    See also:
    http://barton.ebi.ac.uk/servers/amas_server.html

     
    BOXSHADE :-
    Pretty Printing and Shading of Multiple-Sequence Alignments
    See also:
    http://www.ch.embnet.org/software/BOX_form.html at EMNet,
    Switzerland

     
    CLUSTALW :-
    Multiply Sequence Alignments 
    See also:
    http://www.ibc.wustl.edu/service/msa/index.html  at
    IBC-Washington U.
    http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html

     
    -BLAST PRINTS :-
    Alternative perspectives on sequence similarity

     
    BAliBASE :-
    A benchmark alignment database for the evaluation of
    multiple alignment program.

     
    *2*BEAUTY :-
    BLAST Enhanced Alignment Utility (see Documentation) at
    Baylor College of Medicine

     
    ComAlign :-
    Combining many multiple alignments in one improved alignment

     
    *2*DIALIGN 2 :-
    Improvement of the segment-to-segment approach to multiple
    sequence alignment

     
    ESPript  (Easy Scripting in PostScript) :-
    Analysis of multiple sequence alignments in PostScript
    Source code and help files can be downloaded via
    anonymous ftp from ftp://ftp.ibps.fr
    A tar file is present in the directory pub/ESPript

     
    -MSA :-
    Multiple Sequence Alignment at Washington U.

     
    *2*Multiple Sequence Alignments :-
    CLUSTAL-W, MAP, and PIMA alignments at Baylor College of Medicine

     
    -PIR-ALN :-
    A database of protein sequence alignments
    Quarterly updates can be obtained by anonymous ftp from the site at
    NBRF.Georgetown.edu  directory [ANONYMOUS.PIR.ALIGNMENT]

     
    ZPRED :-
    MultPredict Secondary Structure of Multiply Aligned Protein
    Sequences ( uses a set of aligned sequences as input ) at
    Ludwig Institute for Cancer Research, UK
    by Zvelebil et al., UK

     
    SISEQ :-
    Manipulation of multiple sequence and large database files for
    common platforms

     
    -JavaShade :-
    Multiple sequence alignment box-and-shading on the World Wide Web.

     
    *2*BEAUTY-X :-
    Enhanced BLAST searches for DNA queries.

    4. Patterns, Motifs & Profiles

    MOTIF :-
    Motifs looks for sequence motifs by searching through proteins for the
    patterns defined the PROSITE Dictionary of Protein Sites and Patterns.
    Motifs can display an abstract of the current literature on each of the 
    motifs it finds.
    See also:
    http://www.motif.genome.ad.jp/  at GenomeNet, Japan
    Motif at GenomeNet, Japan w/ search from Iowa State

     
    PROFILESCAN  :as part of GCG package only.
    ProfileScan uses a database of profiles to find structural and sequence
    motifs in protein sequences.

     
    COILSCAN  :as part of GCG package only.
     CoilScan locates coiled-coil segments in protein sequences. 

     
    HTHSCAN  :as part of GCG package only.
    HTHScan scans protein sequences for the presence of helix-turn-helix 
    motifs, indicative of sequence-specific DNA-binding structures often 
    associated with gene regulation.

     
    SPSCAN  :as part of GCG package only.
    SPScan scans protein sequences for the presence of secretory 
    signal peptides (SPs). 

     
    PROSITE :-
    Protein Sites and Patterns Database at ExPASy, Switzerland,
    Release 14.0 (11/97) - as part of GCG package.
    See also:
    http://www.expasy.ch/prosite/
    PrositeScan at ISREC, Switzerland 
    PROSITE-Search at EMBL-Heidelberg

     
    PROFILEMAKE  :as part of GCG package only.
    ProfileMake creates a position-specific scoring table, called a profile,
    that quantitatively represents the information from a group of aligned 
    sequences.  The profile can then be used for database searching 
    (ProfileSearch)  or a sequence alignment (ProfileGap).

     
    PROFILEGAP  :as part of GCG package only.
    ProfileGap makes an optimal alignment between a profile and one or
    more sequences.

     
    *2*BLOCKS SEARCH :-
    Search the BLOCKS database.
    BLOCKS Search by e-mail.

     
    BLITZ-Search   :-
    Fast Search at EBI

     
    FASTPAT :-
    FASTA-based Pattern Database Search (see Documentation) at
    Baylor College of Medicine

     
    *3*HPT :-
    Protein Sequence Pattern Recognition in the PIR Database and
    HPT-Homologyat MIPS, Germany

     
    MatrixPlot :-
    Visualizing sequence constraints

     
    *2*PatternFind :-
    Search the SwissProt and Genpept Protein Sequence Databases
    with a PROSITE-formatted Pattern at ISREC, Switzerland

     
    *3*PMOTIF :-
    Search Protein Motifs in Gene Sequence at U. Minnesota

     
    PRINTS :-
    Protein Motif Fingerprints Database and
    PRINTS-ALIGN at UCL-London, UK and

     
    *3*ProfileScan  :-
    Search a Sequence Against a Library of Profiles at ISREC, Switzerland

     
    REPRO :-
    Recognition of Protein Sequence Repeats at EMBL-Heidelberg

     
    *2*Class II MHC quantitative binding motifs :-
    Derived from a large molecular database with a versatile iterative
    stepwise discriminant analysis meta-algorithm


    5. Phylogenetic Analysis

    OUTDISTANCES :as part of GCG package only.
    OutDistances makes a table of the pairwise similarities within a
    group of aligned sequences.

     
    PAUPSEARCH :as part of GCG package only.
    PAUPSearch provides a GCG interface to the tree-searching options in
    PAUP (Phylogenetic Analysis Using Parsimony).  Starting with a set of
    aligned sequences, you can search for phylogenetic trees that are optimal
    according to parsimony, distance, or maximum likelihood criteria;
    reconstruct a neighbour-joining tree; or perform a bootstrap analysis.
    The program PAUPDisplay can produce a graphical version of a 
    PAUPSearch trees file.

     
    PAUPDISPLAY : as part of GCG package only.
    PAUPDisplay provides a GCG interface to tree manipulation, diagnosis, 
    and diaplay options in PAUP (Phylogenetic Analysis Using Parsimony). 
    Starting with a trees file that contains a sequence alignment and one or
    more trees reconstructed from this alignment (such as the output from 
    PAUPSearch), you can plot the tree(s); compute the score of the tree(s); 
    according to the criteria of parsimony, distance or maximum likelihood;
    or calculate a consensus tree (two or more input trees).  PAUPDisplay can
    also plot the trees from a GrowTree trees file.

     
    DISTANCES : as part of GCG package only.
    Distances creates a table of the pairwise distances within a group of 
    aligned sequences.

     
    GROWTREE :as part of GCG package only.
    GrowTree creates a phylogenetic tree from a distance matrix created by 
    Distances using either the UPGMA or neighbour-joining method.  You 
    can create a text of graphics output file.

     
    DIVERGE : as part of GCG package only.
    Diverge estimates the pairwise number of synonymous and nonsynonymous 
    substitutions per site between two or more aligned nucleic acid sequences 
    that code for proteins.  It uses a variant of the mtheod published by Li et.al.

     
    PHYLIP : 
    http://evolution.genetics.washington.edu/phylip.html 
    Programs for inferring phylogenies at University of Washington.
    WebPhylip at Singapore.

     
    -CoPE :-
    A collaborative pedigree drawing environment

     
    *2*TreeGen :-
    Tree Generation from Distance Data at ETH-Zürich, Switzerland

     
    *1*WIT :-
    Is a WWW based system to support the curation of function assignments
    made to genes and the development of metabolic models
    from MCS-Computational Biology at Argonne National Laboratory

     
    Phylogeny Packages
    at EMBNet

     
    GeneTree :-
    Comparing gene and species phylogenies using reconciled trees

     
    *2*HICLAS :-
    A taxonomic database system for displaying and comparing
    biological classification and phylogenetic trees.

     
    DnaSP Version 3 :-
    An integrated program for molecular population genetics
    and molecular evolution analysis.


    6. Secondary Structure Prediction

    PEPPLOT  :as part of GCG package only.
    PepPlot plots measures of protein secondary structure and 
    hydrophobicity in parallel panels of the same plot. 

     
    PEPTIDESTRUCTURE  :as part of GCG package only.
    PeptideStructure makes secondary structure predictions for a peptide
    sequence. The predictions include (in addition to alpha, beta, coil, and 
    turn) measures for antigenicity, flexibility, hydrophobicity, and surface
    probability. PlotStructure displays the predictions graphically. 

     
    PLOTSTRUCTURE  :as part of GCG package only.
    PlotStructure plots the measures of protein secondary structure in the 
    output file from PeptideStructure. The measures can be shown on parallel 
    panels of a graph or with a two-dimensional "squiggly" representation. 

     
    MOMENT  :as part of GCG package only.
    Moment makes a contour plot of the helical hydrophobic moment of a 
    peptide sequence. 

     
    HELICALWHEEL  :as part of GCG package only.
    HelicalWheel plots a peptide sequence as a helical wheel to help you 
    recognize amphiphilic regions. 

     
    *1*nnPredict :-
    Predict Protein Secondary Structure  by Kneller, Cohen & Langridge,
    at UCSF USA

     
    *1* PHD (PredictProtein) :-
    A neural network method for a single sequence or an alignment
    Predict Protein Secondary Structure, solvent accesibility &
    transmembrane segments
    by Rost & Sander, at EMBL-Heidelberg
    PHD by e-mail  w/ search from Iowa State

     
    -PREDATOR:-
    Protein secondary structure prediction from single sequence
    by  Frishman & Argos, EMBL, Germany

     
    *2*SSPRED :-
    Predict the Secondary Structure of Proteins
    (from one sequence or an alignment)  Mehta, Heringa & Argos,
    at EMBL-Heidelberg, Germany
    http://www.mrc-cpe.cam.ac.uk/jong/predict/sspred.htm

     
    -NPS@ :-
    Network Protein Sequence Analysis
    for improved performance in protein secondary structure
    prediction by inhomogeneous score combination.

     
    A new criterion to classify globular proteins based
    on their secondary structure contents.
    This program is available on request from the author

     
    *1*JPred :-
    A consensus secondary structure prediction server.


    7. Hydrophilicity / Hydrophobicity

    PEPPLOT  :as part of GCG package only.
    PepPlot plots measures of protein secondary structure and 
    hydrophobicity in parallel panels of the same plot. 

     
    PEPTIDESTRUCTURE  :as part of GCG package only.
    PeptideStructure makes secondary structure predictions for a peptide
    sequence. The predictions include (in addition to alpha, beta, coil, and
    turn) measures for antigenicity, flexibility, hydrophobicity, and surface
    probability.  PlotStructure displays the predictions graphically. 

     
    PLOTSTRUCTURE  :as part of GCG package only.
    PlotStructure plots the measures of protein secondary structure in the
    output file from PeptideStructure. The measures can be shown on parallel
    panels of a graph or with a two-dimensional "squiggly" representation. 

     
    *2*PSA :-
    Protein Sequence Analysis for Sequences of Unknown Structure
    with options for multimeric and membrane-spanning proteins
    at BMERC/MBCRR  Boston University

     
    TMAP :-
    Identification of Transmembrane Segments on a Protein Sequence at
    Karolinska Institutet

     
    *2*TMpred :-
    Prediction of Transmembrane Regions and Orientation in
    Protein Sequencs at EmbNet, Switzerland

     
    PredAcc :-
    Prediction of solvent accessibility


    8. Nucleic Acid Analysis

    FRAMEALIGN  :as part of GCG package only.
    FrameAlign creates an optimal alignment of the best segment of 
    similarity (local alignment) between a protein sequence and the 
    codons in all possible reading frames of a nucleotide sequence. 
    Optimal alignments may include reading frame shifts.

     
    K-ESTIMATOR
    A program for the calculation of the number of nucleotide 
    substitutions per site and the confidence intervals.
    This program is available for non-profit use via anonymous 
    ftp at ftp.bio.indiana.edu/molbio/mswin

     
    OVERLAP  :as part of GCG package only.
    Overlap compares two sets of DNA sequences to each other in both 
    orientations using a WordSearch style comparison.

     
    NOOVERLAP  :as part of GCG package only.
    NoOverlap identifies the places where a group of nucleotide 
    sequences do not share any common subsequences.

     
    *3*Oligos Parameter Calculation :-
    Calculation of DNA Melting Temperature

     
    *2*Primers! calculator :-
    Calculation of DNA Melting Temperature

     
    -BRAIN (Batch Relevance-based Artificial INtelligence) :-
    Recognition of splice junctions on DNA sequences by BRAIN
    learning algorithm.

     
    A new Fourier transform approach for protein coding measure based
    on the format of the Z curve :
    The program is available on request from C. T. Zhang

     
    *2*MODELTEST:-
    Testing the model of DNA substitution

     
    *3*Sequence Translation :-
    Translate Gene Sequences at U. Minnesota

     
    *2*Translate :-
    Translate a Nucleotide Sequence to a Protein at ExPASy, Switzerland
    and Translateat EBI, UK

     
    -ProbeDesigner :-
    Design of probesets for branches DNA (bDNA) signal amplification assays
    This package is available commercially through the
    Pharmaceutical Drug Discovery program at Chiron Diagnostics

     
    Promoter 2.0 :-
    For the recognition of PolII promoter sequences.

     
    *2*CRAWview :-
    For viewing splicing variation, gene families, and polymorphism
    in clusters of ESTs and full-length sequences.

     
    *3*JaDis :-
    Computing evolutionary distances between nucleic acid sequences.

     
    -Establishing a method of vector contamination identification
    in database sequence.

     
    A RAPID algorithm for sequence database comparisons :-
    Application to the identification of vector contamination in the
    EMBL databases.  This can be downloaded by anonymous ftp
    from ftp://bioinf.man.ac.uk/RAPID


    9. Gene Finding

    TESTCODE  :as part of GCG package only.
    TestCode helps you identify protein coding sequences by plotting
    a measure of the non-randomness of the composition at every third
    base. The statistic does not require a codon frequency table.

     
    CODONPREFERENCE  :as part of GCG package only.
    CodonPreference is a frame-specific gene finder that tries to recognize 
    protein coding sequences by virtue of the similarity of their codon usage
    to a codon frequency table or by the bias of their composition (usually
    GC) in the third position of each codon.

     
    FRAMES  :as part of GCG package only.
    Frames shows open reading frames for the six translation frames of a
    DNA sequence. Frames can superimpose the pattern of rare codon 
    choices if you provide it with a codon frequency table 

     
    TERMINATOR  :as part of GCG package only.
    Terminator searches for prokaryotic factor-independent RNA polymerase
    terminators according to the method of Brendel and Trifonov.

     
    CODONFREQUENCY  :as part of GCG package only.
    CodonFrequency tabulates codon usage from sequences and/or existing
    codon usage tables. The output file is correctly formatted for input to the 
    CodonPreference, Correspond, and Frames programs.

     
    CORRESPOND  :as part of GCG package only.
    Correspond looks for similar patterns of codon usage by comparing codon 
    frequency tables. 

     
    *2*Gene Finder :-
    Predict Gene Structure, Internal Exons and Splicing Sites in
    DNA and Exon-Exon Junstion in cDNA at Baylor College of Medicine

     
    GeneMark :-
    WWW system for prediction of protein coding regions

     
    *3*GenLang :-
    Find Genes and Other Higher-Order Features in Nucleotide
    Sequences at CBIL  -U. Pennsylvania

     
    *1*Grail :-
    Analysis of the Protein Coding Potential of a DNA Sequence
    (see Documentation) at ORNL

     
    GeneScope :-
    Gene recognition by combination of several gene-finding programs


    10. RNA Analysis

    MFOLD : as part of GCG package only.
    MFold predicts optimal and suboptimal secondary structures for 
    an RNA molecule using the most recent energy minimization method 
    of Zuker. 

     
    FOLDRNA : as part of GCG package only.
    FoldRNA predicts a single optimal secondary structure for an RNA 
    molecule by the older method of Zuker.

     
    STEMLOOP : as part of GCG package only.
    StemLoop finds stems (inverted repeats) within a sequence. You specify 
    the minimum stem length, minimum and maximum loop sizes, and the 
    minimum number of bonds per stem. All loops or only the best loops can 
    be displayed on your screen or written into a file. 

     
    PLOTFOLD : as part of GCG package only.
    PlotFold displays the optimal and suboptimal secondary structures for 
    an RNA molecule predicted by MFold. 

     
    *2*VizQFolder :-
    A vector-based method for drawing RNA secondary structure.

     
    -Fast evaluation of internal loops in RNA secondary prediction
        file : zuker.tar.Z

     
    -MIAH :-
    Automatic alignment of eukaryotic SSU rRNAs.

     
    -StemTrace :-
    An interactive visual tool for comparative RNA structure analysis

     
    *2*RNA Movies :-
    Visualizing RNA secondary structure spaces.
    An RNA folding method capable of identifying
    pseudoknots and base triples
    Prediction of RNA secondary structure
    based on helical regions distributions.


    11. Primer Selection

    OLIGO  :-
    A multi-functional program that searches for and selects oligonucleotides
    from a sequence file for polymerase chain reaction (PCR), DNA sequencing,
    site-directed mutagenesis, and various hybridization applications. It calculates
    hybridization temperature and secondary structure of oligonucleotides based 
    on the nearest neighbor thermodynamic values.

     
    *2*Primer :-
    Select PCR Primers in a Gene Sequenceat WICGR-MIT and
    Primer at U. Minnesota

     
    *2*STS Pipeline :-
    Analysis and STS Primer Picking of Short DNA Sequences with
    Duplicate Checking, Sequence Repeat Finding, Restriction Analysis,
    Vector Identification and BLAST Searching at MIT

     
    -A computer driven approach to PCR based differential screening,
    alternative to differential display

     
    GeneDN :-
    for high-level expression design of heterologous genes in a
    prokaryotic syste.
    Source code and related material avialable upon request


    12. Integrated Sequence Analysis

    COMPOSITION : as part of GCG  package
    Composition determines the composition of sequence(s). For nucleotide 
    sequence(s), Composition also determines dinucleotide and trinucleotide 
    content.

     
    ANTHEPROT  :-

     
    -IMAGENE :-
    An integrated computer environment for sequence annotation
    and analysis.

     
    -dg3dseq :-
    Application of distance geometry to 3D visualization of sequence
    relationships.

     
    -TargetFinder :-
    Searching annotated sequence databases for target genes of
    transcription factors.

     
    -PROF (Son of DSC) :-
    For either a single sequence or an alignment.
    developed by Mohammed OUALI and Ross D. KING,
    Imperial Cancer Research Fund, London

     
    *3*Shufflet :-
    Shuffling sequences while conserving the k-let counts

     
    *2*PASSML :-
    Combining evolutionary inference and protein secondary
    structure prediction.

     
    -FT :-
    A Web server to locate periodicities in a sequence.

     
    -VHMPT :-
    A graphical Viewer and editor for Helical Membrane
    Protein Topologies