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Sequence
Analysis:
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BankIt: Submit sequences to
GenBank
Genome Browser:
Search for a sequence on human genome
MGRC:
Malaysian Genomics Resource Centre
Phred:
Reads sequence trace data, make base calls and assigns quality values
Phrap:
Program to assemble DNA sequences
Consed:
View and edit sequences to be used in conjunction with Phred and Phrap
PolyPhred:
For identification of SNPs from trace data
Improbizer:
Searches for motifs in DNA or RNA sequences that occur
with
improbable
frequency
Restriction
mapper:
Graphical restriction map drawing tool
Repeat Masker:
Screens DNA sequences against a library of repetitive elements
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and returns a masked
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query sequence as well as a table annotating the masked regions
Reverse
Complement:
Converts a DNA sequence into its
reverse, complement, or
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-
given DNA sequence
Codon Usage:
Search the codon usage in various species
Ident and Sim:
Accepts a group of aligned
sequences and calculates the identity and similarity
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Sequence Comparison:
BLAST at
CBIL:
Search for an
input sequence in a database
Blast at
NCBI:
Search between an input sequence in a database
NCBI-BLAST2 at
EMBL:
Find regions of sequence similarity
WU-BLAST2 at EMBL:
Search with post-processing at EMBL
PSI-Blast at
NCBI:
Position specific BLAST
FASTA3: Search
between an input sequence in a database
BLAT:
BLAT Search Human Genome at UCSC
Human/Mouse
Homology:
Identify mouse / human orthologs
SAM:
Sequence alignment and modeling system
MPSRCH: Comparison using Smith & Waterman
algorithm
Sequence
Alignment:
BoxShade:
Printouts from multiple-aligned sequences
ClustalW:
Multiple sequence alignment
CINEMA:
Colour interactive editor for multiple alignments
FLAG:
Fast Local Alignment
for Gigabases
Malign: Multiple sequence alignment
MultAlin:
Multiple sequence alignment by Florence Corpet
MUMmer:
Alignment of
large scale DNA and Proteins
Pair
Alignment: Pairwise sequence
alignment
ParAlign:
Sequence search
PipMaker: Aligns
similar regions in two DNA sequences
SIM4: a program to
align cDNA
and genomic DNA
STRETCHER:
Best global alignment between two sequences
YASS: DNA local alignment program
Sequence Analysis
Servers:
Analysis Tool:
Several good sequence analysis
tools
BCM: Baylor college of medicine search
launcher
BIRCH:
A resource for molecular sequence analysis
EMBnet:
Sequence analysis tools
Prediction
Servers:
Lots of tools
Sequence Manipulation
Suite:
Programs for analysis of DNA & proteins
Tools at
EBI: Many
analysis tools
WorkBench: Tools for
protein and nucleic acid analysis
Subcellular
Localization:
ChloroP: predicts the presence of chloroplast transit
peptides
iPSORT:
Predictor for N-terminal sorting signals
MitoProt:
Prediction of mitochondrial targeting
sequences
PredictNLS:
Determination of Nuclear Localization Signals
Predotar:
Mitochondrial and
plastid targeting sequences
PSORT:
Subcellular localization of proteins
SignalP:
Protein signal prediction
SubLoc:
Prediction of Protein Subcellular Localization
TargetP:
Prediction of subcellular location
siRNA
Design Softwares:
Ambion
Dharmacon
SFold
SiRNA
Target finder
Sequence Manipulation
Utilities:
Sequence
manipulation utilities
Sequence Massager:
Format and manipulating nucleic acid sequences
Transmembrane
Prediction:
DAS: Transmembrane sequence
prediction
HMMTOP:
Prediction of transmembrane helices
TMAP:
Membrane protein prediction
TMHMM:
Transmembrane helices in proteins
TopPred:
Topology prediction of membrane proteins
TMPred:
Prediction of transmembrane regions and orientation
Tutorials:
Learning page:
Go to our learning page for analysis
tutorials
Exon & ORF
Prediction:
AAT: Analysis and Annotation
Tool
DioGenes:
Find protein-encoding regions in genomic sequences
Doublescan:
Comparative prediction of protein coding genes
FirstEF: First-exon
& promoter prediction program
GeneID:
Gene identification and structure prediction
Generation:
Microbial gene prediction system
GeneSeqer:
Identify exon/intron structure in pre-mRNA
Genie:
Gene finder based on hidden Markov models
GenomeScan: Based on
GenScan incorporating protein homology
GenScan:
Identification of gene structures in genomic DNA
GenViewer:
Predicting of protien-coding gene structures
GlimmerM:
A system for finding genes in microbial DNA
HMMGene: Prediction
of vertebrate and C. elegans genes
MetaGene: submit sequences to
seven gene prediction engines
MZEF:
Predict protein coding exons in genomic DNA
NetGene2:
Neural network predictions of splice sites
ORF
Finder:
Search for open reading frame, at NCBI
SplicePredictor:
Identify potential splice sites in plant pre-mRNA
SpliceSite
Prediction:
Splice site prediction by neural network
Wise2 :
Intelligent algorithm for DNA searches
WebGene: Several tools
for prediction and analysis gene structures
Genome
Analysis & Annotation:
AGAVE:
Architecture for Genomic Annotation, Visualization and Exchange
ENSEMBL:
Several eukaryotic genomes
FANTOM:
Functional annotation of the mouse
Flybase:
Drosophila genome
GAIA22:
Genome annotaion for chromosome 22 at upenn
Genquire:
Genome browser
Genome
Browser:
Human genome browser at UCSC
GRL:
Gene Resource Locator maps of EST to genome
NCBI:
Several species
SGD:
Saccharomyces Genome database
UCSC: The UCSC
Genome Bioinformatics - Human, Mouse & Rat
Wormbase: C. elegans genome
Gene Annotation Tools:
GoMiner: Annotates genes to gene ontology
ids |
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Protein Sequence
Analysis:
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Allermatch
Compare the amino acid sequence of allergens
Proteomics Tools:
Several
useful tools for protein analysis
PAPIA:
Protein
sequence homology, structure similarity, multiple alignement, secondary structure
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and
transcription factor binding site prediction
SAWTED:
Detection of remote homologues PSI-BLAST and fold recognition
Molecular
Weight:
Calculates the molecular weight of a protein
Protein Stats:
Calculate the aminoacid composition of a protein
Protein Translation:
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that can
be used to find regions of minimal degeneracy
at the nucleotide level
One to three:
Convert single letter code to three letter code
Three to
one:
Convert three letter code to single letter code
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Protein Domains, Motifs and
Signatures:
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Blocks:
Search DNA or protein sequence against a Blocks
database
DomainParser:
A protein domain partition program
eMotif:
Search for an input pattern
eBlocks:
Database of protein sequence blocks
InterProScan:
Query your protein sequence against InterPro
MEME:
Motif discovery tool
MAST:
Motif alignment and search tool
Motif:
Search a protein motif in Prosite pattern or profile, Blocks,
ProDom, Prints,
Pfam
databases or
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DNA motif in Transfac database or a user
defined database
PatScan:
Search a pattern in protein/nucleic acid database
PatternSearch: Search a pattern against protein
databases
Pfam:
Classification of protein families
PRINTS:
Search against a protein finger print database
ProDom:
The protein domain database
ProfileScan:
Search for a protein profile
Prosite:
Search a motif against Prosite database
SMART:
Simple modular architecture research tool
Swiss-Prot/TrEMBL:
Protein sequence database
VAST:
Comparison of 3-dimensional protein structures
Phylogeny:
FastDNAml:
DNA phylogenetic trees using maximum likelihood
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
Protein Secondary Structure
Prediction:
3D-PSSM:
Protein Fold Recognition
COILS:
Prediction of Coiled Coil Regions in Proteins
Folding@home
: Protein folding
GOR/DSC/PHD/PREDATOR/SIMPA:
Several tools
MARCOIL:
Prediction of coiled-coil domains in protein sequences
PredictProtein: Sequence analysis and
structure prediction
SAPS:
Statistical analysis of protein sequences
SSCP:
Predicts helix, strand, and coil for a given protein
VAST: Structure-structure similiarity
search
Promotor & Transcription
Regulation:
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-
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Pol II promoter sequences
SignalScan:
Find homologies of published signal sequences
TESS:
Transcription element search system
Tfsearch:
Searching Transcription Factor Binding Sites
Protein 3D Structure /
Modelling:
FUGUE:
Sequence-structure homology recognition
GeneMine:
Sequence analysis and visulization tool
PDB Viewer:
Protein structure database
Proinformatix:
Modeling oligopeptides for energetically minimized structures
LG-SCORE: Calculate the quality of 3D model
Protein Modifications:
NetOGlyc 2.0:
Glycosylation prediction
NetPhos 2.0:
Phosphorylation prediction
big-PI
Predictor:
GPI
anchor prediction
Proteomics / Mass Spectrometry
Tools:
- Prospector: Proteomics tools for
mining sequence databases in conjunction with
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mass spectrometry
Prowl: Software
for protein mass spectrometry
Protein
Splicing: InBase: Inteins in sequenced
genes
Primer Design:
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CodeHop:
PCR primers designed from protein multiple sequence alignments
ExonPrimer:
Design intronic primers for the PCR amplification of exons
GeneFisher:
Interactive PCR primer design
PCR Links:
PRIDE:
Primer design programs developed for the large scale design
Primer
Generator:
Automated primers for site directed
mutagenesis
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RNA Secondary Structure
Prediction:
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MFold: A program to predict RNA secondary
structure
RNA 2
Structure: Predict RNA secondary
structure
SFold:
Statistical folding & rational design
of nucleic acids
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Molecular
Modeling:
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CMM: Center for molecular modelling at
NIH
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Alternate Splicing
Analysis:
ASAP: Alternate splicing analysis tool at
UCLA
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Transcriptional
Profiling:
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Go to
Computers and
programming
to find free
softwares
Others:
Jemboss
Oligo Localizer:
Localizes an oligonucleotide on a DNA
sequence
High Throughput
Data Handler:
serval tools
Sequence cleaner
Sequence
randomizer
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