Very Useful Multipurpose Software Packages

The Sequence Manipulation Suite A comprehensive sequence analysis package
EMBOSS A suite of free software tools for sequence analysis
ExPaSy Proteomics Tools Useful tools for protein analysis
DeCypher Easy access to a variety of nucleic acid and protein analysis packages



Sequence Search

NCBI BLAST Compare a nucleic acid or protein sequence against database
EMB BLAST Permits one to specifically search databases
WU BLAST A powerful software package for gene and protein identification
FASTA33 Provides sequence similarity and homology searching against nucleotide and protein databases using the Fasta3 programs



Sequence Alignment

BLAST-2 Produces the alignment of two given sequences using BLAST engine for local alignment
Pairwise FLAG Performs local alignment for two different DNA sequences
SCAN2 Alignment of genome length DNAs
Advanced PipMaker Aligns two DNA sequences
CoreGenes Determines the core set of genes in a maximum of five small genomes
ALIGN Query Compares two sequences
LALIGN Finds multiple matching subsegments in two sequences
ClustalW Multiple Sequence Alignment
DbClustal Aligns sequences from a BlastP database search with one query sequence
MultAlin Multiple sequence alignment
Multiple Alignment This service also provides phylogenetic analysis of the data
DiAlign DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences
BOXSHADE Accepts a wide variety of file formats and allows the requester considerable flexibility in defining the output appearance
CINEMA Colour INteractive Editor for Multiple Alignments for DNA and proteins
Multiple Align Show accepts a group of aligned sequences (in FASTA or GDE format) and formats the alignment to your specifications



Phylogeny

FastDNAml Construction of phylogenetic trees of DNA sequences using maximum likelihood method
Phylip Several phylogeny and tree drawing programs
PhylogeneticTree Phylogenetic tree prediction
Phylogeny Programs: Multiple methods available
Tree of Life Information about phylogeny and biodiversity
TreeGen Tree generation from distance data
TreeTop Phylogenetic Tree Prediction



Transcription Elements

Cister Cis-element Cluster Finder
CONPRO CONsensus PROmoter predictor
Dragon Drogon Promoter finder
MatInspector Detection of transciption factor binding sites
Promotor Scan Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences
SignalScan Find and list homologies of published signal sequences with the input DNA sequence
TATA prediction Predict TATA signal in eukaryotic genes
TESS Transcription element search system
Tfsearch Searching Transcription Factor Binding Sites
Promoter Inspector Prediction of promoter regions in mammalian genomic sequences
Promotor Prediction Neural network promoter prediction



Gene Prediction

ORF Finder Search for open reading frame, at NCBI
FGENEH Splice sites, protein coding exons and Gene models construction, promotor and poly-A search
Gene Finder Predict protein coding exons in genomic DNA
GeneID Gene identification and structure prediction
GeneMark Inhomogeneous Markov model approach combined with training datasets to predict genes
GeneParser2 Identification of protein coding regions
Generation Microbial gene prediction
Genie Gene finder based on hidden Markov models
GenLang Linguistics based method to find genes
GenScan Identification of gene structures in genomic DNA
GenViewer Predicting and analysis of protien-coding gene structures
Glimmer A system for finding genes in microbial DNA
Grail DNA sequence analysis tool
HMMGene Prediction of vertebrate and C. elegans genes
NetGene2 Neural network predictions of splice sites
Procrustus Gene recognition via spliced alignment
SpliceSite Prediction Splice site prediction by neural network
Wise2 Intelligent algorithm for DNA searches
WebGene Several tools for prediction and analysis of protein coding gene structures
Xgrail Find exons and other features



Gene Expression

BRB ArrayTools An integrated package for the visualization and statistical analysis of DNA microarray gene expression data
Eisen Lab Tools ScanAlyze, Cluster, TreeView
TIGR ArrayViewer Designed to facilitate the presentation and analysis of microarray expression data
XCluster Clustering tool from Stanford
ClustArray clusters expression data and produces an annotated graphical visualization of the clusters



PCR Related

Primer3 A very powerful PCR primer design program
GeneFisher A very good site allowing great control over primer design
CODEHOP PCR primers designed from protein multiple sequence alignments
PRIDE Primer design for large-scale projects in sequencing, PCR, and DNA array design
DoPrimer Not abailable
Oligo Analyzer Primer selection program by IDT
Poland Calculate the thermal denaturation profile of double-stranded RNA, DNA or RNA/DNA-hybrids based on sequence input and parameter settings in this form.
DAN Calculates DNA RNA/DNA melting temperature (EMBOSS)
Biopolymer Calculator Calculates molecular weight, melting temperature
Oligonucleotide Properties Calculator Oligonucleotide Properties Calculator



Oligonucleotide Structure

Vienna RNA secondary structure prediction Predict secondary structures of single stranded RNA or DNA sequences
MFold Predict DNA or RNA structure
ICGEBnet A collection of methods which graphically represent various DNA parameters
model.it Produces a 3D model of DNA molecule given a sequence of maximum 700 nucleotides
Sequence-Directed DNA Curvature Gives an elegant output which requires a VRML plug-in and converter for visualizing and manipulating the results
RNA secondary structure Prediction Predict RNA secondary structure
SStructView RNA Secondary Structure Java Applet



Oligonucleotide repeats

Oligonucleotids repeats finder Finds direct, direct complementary, symmetric and invert repeats
REPuter Fast computation of maximal repeats in complete genomes
EINVERTED Finds DNA inverted repeats
PALINDROME Looks for inverted repeats in a nucleotide sequence (EMBOSS)
EQUICKTANDEM Finds tandem repeats (EMBOSS)
Repeat Masker Screens DNA sequences against a library of repetitive elements and returns a masked query sequence as well as a table annotating the masked regions



Other Oligonucleotide Analysis Tools

Nucleic Acid Sequence Massager Format and manipulating nucleic acid sequences, reverse, complement, etc.
Readseq Biosequence conversion tool
VecScreen Screens your DNA sequence for potential vector sequence
WORDCOUNT Counts words of a specified size in a DNA sequence (EMBOSS)
Cumulative GC-Skew Take a DNA sequence and calculates %GC percentage, GC-skew or cumulative GC-skew using a user defined window
CAP3 Contig Assembly Program
ERR_WISE Detection of Frameshift Sequencing Error
Wise2: DNA vs Protein Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors
CloneIt An online program finding sub-cloning strategies,in-frame deletions and frameshifts using restriction enzymes and DNA polymerases
Physical Mapping Calculator Shows how the library redundancy and %% of genome covered depends on the number of clones in a library
Webcutter Restriction endonuclease digestion
Restriction Site Analysis Provides one with considerable choice of enzymes and output format.
Reverse Complement Converts a DNA sequence into its reverse, complement, or reverse-complement
Phred/Phrap/Consed Phres: Reads sequence trace data, make base calls and assigns quality values. Phrap: Program to assemble DNA sequences
Improbizer Searches for motifs in DNA or RNA sequences that occur with improbable frequency
Filter DNA Removes non-DNA characters from text
GenBank to Fasta Convert GenBank input to fasta format
DNA Analyzer Multipurpose DNA analyzer
Nucleic acid calculator From A260nm calculate DNA, RNA and oligonucleotide concentrations online



Translation

Reverse Translate a Protein Enter a protein sequence and obtain its reverse translation for use in design of degenerate oligonucleotides. The program uses the standard genetic code and does not consider differences in codon usage
Backtranslation Provides one with a wealth of options include organism-specific codon usage
Reverse Translator Changing a specific amino acid into another
ExPASy Translate tool Useful if you have a gene which begins with an alternative start codon.
Third Position GC Skew Display Predicts genes by comparing possible open reading frames (variety of initiation codon options) to a third position GC plot. This tool is apparently most effective for genomes with a high G+C content
Reverse Translate Accepts protein sequence and uses a codon usage table to generate a graph that can be used to find regions of minimal degeneracy at the nucleotide level



Protein Secondary Structure (including sub-cellular localization)

Structure Prediction Meta-server Runs PDB-Blast, ORFeus, FFAS, 3D-PSSM, GenTHREADER, mGenTHREADER, INBGU, ShotGun-INBGU, Sam-T99, FUGUE2, SUPERFAMILY, Jpred2, and PsiPred.
VAST Structure-structure similiarity search
PSA The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence
PredictProtein PredictProtein is a service for sequence analysis, and structure prediction
JPred A consensus method for protein secondary structure prediction
NPSA Provides different methods for protein secondary structure prediction
Folding@home Protein folding
Multicoil Predict coiled coil structures
MultPredict Secondary Structure of Multiply Aligned Sequences
NNPredict Protein secondary structure prediction
Predator Secondary structure prediction
PredictProtein Sequence analysis and structure prediction
SSCP Predicts helix, strand, and coil for a given protein
SSPSI Threading program for protein secondary structure
ToPLign Alignment and structure prediction by threading
SOSUI Secondary structure prediction of membrane proteins
TMpred Prediction of Trans-membrane Regions and Orientation
TMHMM Prediction of transmembrane helices in proteins
DAS Transmembrane Prediction Server
TopPred Topology prediction of membrane proteins
SignalP Protein signal prediction
TargetP Prediction of subcellular location
PSORT A series of programs for the prediction of protein localization sites in cells. Choose programs specific for for animal, yeast, plant or bacterial proteins
SIGFIND2 Predicts signal peptides at the start of eukaryotic protein sequences or searches open reading frames with a potential signal peptide coded in nucleotide sequences
ProtComp Can be used to predict the subcellular localization for animal/fungal and plant proteins



Protein Tertiary Structure

SWEET Constructs 3D model of saccharides from their sequences using standard nomenclature
3D-PSSM Protein Fold Recognition using 1D and 3D Sequence Profiles coupled with Secondary Structure and Solvation Potential Information
SWISS-MODEL An automated comparative protein modelling server
SDSC1 SDSC Protein Structure Homology Modeling
3D-JIGSAW Builds three-dimensional models for proteins based on homologues of known structure
WHAT IF Offers one a large number of tools for examining PDB files
PDB2MultiGIF Takes the 3D structure and generates an animated image which can be displayed using any browser
FUGUE Sequence-structure homology recognition
Proinformatix Modeling oligopeptides for energetically minimized structures



Protein Domain, Motif

Blocks Search DNA or protein sequence against a Blocks database
DomainParser A protein domain partition program
PatternSearch Search a pattern against protein databases
ProfileScan Search for a protein profile
MEME Motif discovery tool
MAST Motif alignment and search tool
VAST Comparison of 3-dimensional protein structures
SMART Simple modular architecture research tool
Prosite Search a motif against Prosite database
Pfam Classification of protein families
Motif Search a protein motif in Prosite pattern or profile, Blocks, ProDom, Prints, Pfam databases or DNA motif in Transfac database or a user defined database
PRINTS Search against a protein finger print database
ProDom The protein domain database
PatScan Search a pattern in protein/nucleic acid database
InterProScan Includes Pfam, Prosite and Prints
PANAL Searches Prosite patterns & profiles, BLOCKS, PRINTS and Pfam
eMATRIX Includes these sites and PRODOM, and DOMO databases.
CDD (Conserved Domain Databases) Includes Smart and Pfam and is invoked when one uses BLASTP
Pfam HMM Analyze a query sequence by searching Pfam HMMs
Scan a protein sequence for the occurrence of patterns and profiles stored in the PROSITE database, or to search protein databases with a user-entered pattern
fingerPRINTScan Consult PRINTS for further information on the motifs



Protein Modification

NetOGlyc 2.0 Glycosylation prediction
NetPhos 2.0 Phosphorylation prediction
big-PI Predictor GPI anchor prediction
FindMod Predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides
GlycoMod Predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses



Other Protein Analysis Tools

One to three Convert single letter code to three letter code
Three to one Convert three letter code to single letter code
ProtScale Allows you to compute and represent the profile produced by any amino acid scale on a selected protein.
SAPS Statistical Analysis of Protein Sequences
ProtParam tool Allows the computation of various physical and chemical parameters for a given protein
Compute pI/Mw tool Allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight)
PEPSTATS Protein statistics
CYSREDOX Calculate the redox state of cysteine residues in proteins
CYSPRED Predictor of bonding state of cysteines in proteins
Cutter Cutter is a program that allows to generate peptide fragments by the enzymatic or chemical cleavage of a protein sequence
FLICKER Comparing images, such as two 2-D gels from different Internet sources on your Web browser
K2d Prediction of percentages of protein secondary structure from CD spectra
MOWSE Molecular weight search against a peptide mass database