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 :-

TagIdent tool (formerly GuessProt) :-

PROPSEARCH :-

PEPTIDESEARCH:-

MPCT :-

PEPTIDEMASS :-

pI/Mw :-

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 :-

PepPepSearch :-

PROPSEARCH :-

Family Pairwise Search :-

WebBLAST 2.0 :-

Blocks+ :-

EDITtoTREMBL :-

A novel method for automatic functional annotation

KIND (Karolinska Institutet Nonredundant Database) :-

WWW access to the SYSTERS

ParAlign and SWMMX :-

SAM-T98  (Sequence Alignment and Modeling) :-

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 :-

Dotlet :-

SSEARCH :-

SSP :-

SAPS:-

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 :-

BAliBASE :-

BEAUTY :-

ComAlign :-

DIALIGN 2 :-

ESPript  (Easy Scripting in PostScript) :-

MSA :-

Multiple Sequence Alignments :-

PIR-ALN :-

ZPRED :-

SISEQ :-

JavaShade :-

BEAUTY-X :-

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.

BLITZ-Search   :-

FASTPAT :-

HPT :-

MatrixPlot :-

PatternFind :-

PMOTIF :-

PRINTS :-

ProfileScan  :-

REPRO :-

Class II MHC quantitative binding motifs :-

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 :-

TreeGen :-

WIT :-

Phylogeny Packages

GeneTree :-

HICLAS :-

DnaSP Version 3 :-

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.

nnPredict :-

PHD (PredictProtein) :-

PREDATOR:-

SSPRED :-

NPS@ :-

A new criterion to classify globular proteins based

JPred :-

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.

PSA :-

TMAP :-

TMpred :-

PredAcc :-

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.

Oligos Parameter Calculation :-

Primers! calculator :-

BRAIN (Batch Relevance-based Artificial INtelligence) :-

A new Fourier transform approach for protein coding measure based

MODELTEST:-

Sequence Translation :-

Translate :-

ProbeDesigner :-

Promoter 2.0 :-

CRAWview :-

JaDis :-

Establishing a method of vector contamination identification

A RAPID algorithm for sequence database comparisons :-

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.

Gene Finder :-

GeneMark :-

GenLang :-

Grail :-

GeneScope :-

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.

Fast evaluation of internal loops in RNA secondary prediction

MIAH :-

StemTrace :-

RNA Movies :-

An RNA folding method capable of identifying

Prediction of RNA secondary structure

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.

Primer :-

STS Pipeline :-

A computer driven approach to PCR based differential screening,

GeneDN :-

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 :-

dg3dseq :-

TargetFinder :-

PROF (Son of DSC) :-

Shufflet :-

PASSML :-

FT :-

VHMPT :-