BankIt:
Submit sequences to GenBank
Genome Browser:
Search for a sequence on human genome
MGRC:
Malaysian Genomics Resource Centre
Sequence
Pattern Finder:
Locates sequences matching a particular pattern in a given DNA sequence
Restriction
mapper: Graphical restriction map drawing tool
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
Reverse
Complement: Converts a DNA sequence into its reverse,
complement, or reverse-complement
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
RepeatMasker:
screens DNA sequences against a library of repetitive elements and
returns a masked query sequence
Shuffle:
Radomize a input 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 of each sequence pair
Filter
DNA: Removes non-DNA characters from text
GenBank
to Fasta: Convert GenBank input to fasta format
CpG
Islands: Searches for CpG islands in DNA
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
HMMER : Profile hidden Markov
models for sequence analysis
MPSRCH:
Comparison using Smith & Waterman algorithm
PepPepSearch:
Search SwissProt for a peptide sequence
PepPdbSearch:
Search PDB for a peptide sequence
PepDnaSearch:
Search SwissProt for a DNA & peptide sequence
BoxShade: Printouts from multiple-aligned sequences
ClustalW:
Multiple sequence alignment
CINEMA:
Colour interactive editor for multiple alignments
DiAlign:
Multiple alignment
Display: Compares the sequences in an alignment
to its consensus
FLAG: Fast Local Alignment
for Gigabases
Malign: Multiple sequence alignment
MultAlin:
Multiple sequence alignment by Florence Corpet
Multiple Alignement: Multiple sequence
alignment
MUMmer: Alignment of
large scale DNA and Proteins
Pair Alignement: 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 Manipulation Utilities |
Sequence
manipulation utilities
Sequence
Massager: Format and manipulating nucleic acid sequences, reverse,
complement, etc.
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
| Promotor & Transcription Regulation: |
Cis-Site
Seeker: Binding sites for regulatory proteins
Cister:
Cis-element Cluster Finder
CONPRO:
CONsensus PROmoter predictor
Dragon: Drogon Promoter
finder
E. Coli DNA binding
site
Eponine: Tool to
detect mammalian transcription start sites
FIE: 5' End Information
Extraction
FirstEF: First-exon
& promoter prediction for human DNA
Fly Enhancer: search engine to find
clusters of binding sites
MarFinder:
Deduce the presence of matrix association regions
MatInspector:
Detection of transciption factor binding sites
Matix
Search: Find and list homologies of published signal
sequences in the IMD database with the input DNA sequence
NeuralNet
promoter perdiction:
Promotor
Scan: Promoter regions based on scoring homologies with
putative eukaryotic Pol II promoter sequences
SignalScan:
Find homologies of published signal sequences
TATA
prediction: Predict TATA signal in eukaryotic genes
TESS:
Transcription element search system
Tfsearch:
Searching Transcription Factor Binding Sites
Promoter
Inspector: Promoters in mammalian genomic sequences
Promotor
Prediction: Neural network promoter prediction
TransPath: Pathways involved in
the
regulation of TFs
AAT: Analysis
and Annotation Tool
DioGenes:
Find protein-encoding regions in genomic sequences
Doublescan:
Comparative prediction of protein coding genes
FGENESH:
Splice sites, protein coding exons & gene models
FirstEF: First-exon
& promoter prediction program
GATG ORF finder:
Gene Prediction Using GA/TG dinucleotides
GeneID:
Gene identification and structure prediction
GeneMark:
Markov model with training datasets to predict genes
GeneParser2: Identification of
protein coding regions
Generation:
Microbial gene prediction system
GeneSeqer:
Identify exon/intron structure in pre-mRNA
Genie:
Gene finder based on hidden Markov models
GenLang:
Linguistics based method to find genes
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
Grail:
DNA sequence analysis tool
HMMGene: Prediction
of vertebrate and C. elegans genes
MetaGene: submit sequences to
seven gene prediction engines
MORGAN:
A decision tree system for finding genes
MZEF:
Predict protein coding exons in genomic DNA
NetGene2:
Neural network predictions of splice sites
ORF
Finder: Search for open reading frame, at NCBI
Pombe:
Predict protein coding exons fission yeast
Procrustus:
Gene recognition via spliced alignment
SLAM:
Comparative gene annotation and alignment
SplicePredictor:
Identify potential splice sites in plant pre-mRNA
SpliceSite
Prediction: Splice site prediction by neural network
Twinscan: Comparative
gene prediction
VEIL:
A hidden Markov model for finding genes
Wise2 :
Intelligent algorithm for DNA searches
WebGene: Several tools
for prediction and analysis gene structures
Xgrail:
Find exons and other features
YeastGene:
Measure the coding ability of an ORF in S cerevisiae
| Alternate Splicing Analysis: |
ASAP:
Alternate splicing
analysis tool at UCLA
HASDB:
Human alternative splicing database at UCLA
AsMamDB:
alternatively spliced genes in human, mouse and rat
ASD:
Alternative splicing
database at CSHL
| RNA Secondary Structure Prediction: |
MFold:
A program to predict RNA secondary structure
RNA 2 Structure: Predict RNA secondary
structure
SFold:
Statistical folding & rational design
of nucleic acids
SStruct
View: RNA secondary structure java applet
Ambion
Dharmacon
EMBOSS
OligoEngine
SFold
SiRNA
Target finder
DSSTox
Jemboss
Oligo
Localizer: Localizes an oligonucleotide on a DNA
sequence
High
Throughput Data Handler: serval tools
Sequence
cleaner
Sequence
randomizer
Go to Computers
and programming to find free softwares
|
| Protein Sequence Analysis: |
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 and transcription factor binding site prediction
ALion:
Pair wise sequence aligment
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
Translation Machine at EBI:
Java Ribosome:
Translation tool
Protein
translator: Converts DNA to RNA to protein
Translate Tool:
Translation of a nucleotide sequence to protein
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
One
to three: Convert single letter code to three letter code
Three
to one: Convert three letter code to single letter code
| Protein Domains, Motifs and Signatures: |
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 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
PIR-ALN:
Database
of protein sequence alignment
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
| Transmembrane Prediction: |
DAS:
Transmembrane sequence prediction
HMMTOP: Prediction of
transmembrane helices
SOSUI:
Secondary structure prediction of membrane proteins
TMAP:
Membrane protein prediction
TMHMM:
Transmembrane helices in proteins
TopPred:
Topology prediction of membrane proteins
TMPred:
Prediction of transmembrane regions and orientation
| Subcellular Localization: |
ChloroP:
predicts the presence of chloroplast transit peptides
iPSORT: Predictor for
N-terminal sorting signals
MitoProt: Prediction of mitochondrial targeting
sequences
NNPSL:
Subcellular Location of Proteins by Neural Networks
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
| Protein Secondary Structure Prediction: |
3D-PSSM:
Protein Fold Recognition
Folding@home
: Protein folding
GOR/DSC/PHD/PREDATOR/SIMPA:
Several tools
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
SAPS:
Statistical analysis of protein sequences
SAINT:
Prediction of protein secondary-structure
SOSUI:
Secondary structure prediction of membrane proteins
SSCP:
Predicts helix, strand, and coil for a given protein
SSPSI:
Threading program for protein secondary structure
SSP/NNSSP/SSPAL: Secondary structure
predictions
ToPLign:
Alignment and structure prediction by threading
VAST:
Structure-structure similiarity search
| 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
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 mass
spectrometry
Prowl: Software
for protein mass spectrometry
MOWSE:
Molecular weight search against a peptide mass database
Peptide
Search: Protein identification by peptide mapping or
peptide sequencing
InBase:
Inteins in sequenced genes
CMM: Center
for molecular modelling at NIH
| Transcriptional Profiling: |
Go to Microarrays
& differential display page
| Genome Analysis & Annotation: |
AGAVE:
Architecture for Genomic Annotation, Visualization and Exchange
Chr22
promotors: Chr22 promotor annotation sfrom
Genomatix
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
Genotator:
Automated sequence annotation
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
| Sequence Analysis Servers: |
Analysis
Tool: Several good sequence analysis tools
BCM:
Baylor college of medicine search launcher
BioComputing:
Links to several sequence analysis tools
BIRCH:
A resource for molecular sequence analysis
EMBnet:
Sequence analysis tools
GANESH: A
Sequence Analysis And Display Package
META
Server: Several protein sequence analysis tools
NPS:
Network protein sequence analysis, France
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
CodeHop:
PCR primers designed from protein multiple sequence alignments
DoPrimer:
ExonPrimer:
Design intronic primers for the PCR amplification of exons
GeneFisher:
Interactive PCR primer design
Oligo Analyzer :
Primer selection program by IDT
Oligo
Calculater:
PCR Links:
PRIDE:
Primer design programs developed for the large scale design
Primer
3: Pick primers from DNA sequence
Primer
Generator: Automated primers for site directed mutagenesis
CIMMaker:
Generates color coded Clustered image maps
CSA:
Correlation search analysis
GoMiner:
Annotates genes to gene ontology ids
GCSP:
General correlation and scatter plot
MatchMiner:
Translates among various gene identifiers from many databases
MedMiner:
Link gene to literature information
Molecular Models:
Chime and RasMol images of the molecules
Learning
page: Go to our learning page for analysis tutorials |
