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Sequence, Structure & Function Analysis

Sequence Analysis - Sequence Comparion - Sequence Alignment - Sequence Manipulation - Phylogeny -Promoter Prediction & Transcription Regulation - Exon & ORF Prediction - Alternate Splicing - RNA Secondary Structure - siRNA Design - Protein Sequence Analysis - Protein Translation - Domains, Motifs and Signatures - Transmembrane Prediction - Subcellular Localization - Protein Secondary Structure Prediction - Protein 3D Structure - Protein Modifications - Proteomics & Mass Spectrometry Tools - Protein Splicing - Molecular Modeling - Transcriptional Profiling - Genome Analysis & Annotation - Sequence Analysis Servers - Gene Annotation - Primer Design - Free Softwares - Tutorials

Sequence Analysis:

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
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

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
Sequence Pattern Finder:    Locates sequences matching a particular pattern in a

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

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

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
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:

ClustalW:   Multiple sequence alignment
Malign:   Multiple sequence alignment
MUMmer: Alignment of large scale DNA and Proteins
   PipMaker: Aligns similar regions in two DNA sequences

Sequence Analysis Servers:

Analysis Tool:    Several good sequence analysis tools
BCM:   Baylor college of medicine search launcher
BIRCH:    A resource for molecular sequence analysis
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
PredictNLS: Determination of Nuclear Localization Signals
PSORT:   Subcellular localization of proteins
SignalP: Protein signal prediction

siRNA Design Softwares:

Dharmacon
SFold

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
TMHMM: Transmembrane helices in proteins

Tutorials:

Learning page:    Go to our learning page for analysis tutorials

Exon & ORF Prediction:

Doublescan: Comparative prediction of protein coding genes
FirstEF: First-exon & promoter prediction program
GeneID:   Gene identification and structure prediction
Genie:   Gene finder based on hidden Markov models
GenScan:   Identification of gene structures in genomic DNA
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
NetGene2:   Neural network predictions of splice sites
ORF Finder:    Search for open reading frame, at NCBI
SpliceSite Prediction:    Splice site prediction by neural network

Genome Analysis & Annotation:

ENSEMBL:   Several eukaryotic genomes
FANTOM: Functional annotation of the mouse
Flybase: Drosophila genome
Genquire: Genome browser
Genome Browser: Human genome browser at UCSC
NCBI: Several species
SGD: Saccharomyces Genome database
UCSC: The UCSC Genome Bioinformatics - Human, Mouse & Rat
Wormbase: C. elegans genome

Protein Sequence Analysis:

Allermatch Compare the amino acid sequence of allergens
Proteomics Tools:    Several useful tools for protein analysis
Molecular Weight:    Calculates the molecular weight of a protein
Protein Stats: Calculate the aminoacid composition of a protein

Protein Translation:

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:

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

Pfam:   Classification of protein families
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:

Phylip: Several phylogeny and tree drawing programs
PhylogeneticTree:   Phylogenetic tree prediction
Phylogeny Programs:    Multiple methods available
Tree of Life: Information about phylogeny and biodiversity
TreeTop: Phylogenetic Tree Prediction

Protein Secondary Structure Prediction:

3D-PSSM:   Protein Fold Recognition
Folding@home : Protein folding
GOR/DSC/PHD/PREDATOR/SIMPA: Several tools
PredictProtein:   Sequence analysis and structure prediction
SAPS:   Statistical analysis of protein sequences VAST:   Structure-structure similiarity search

Promotor & Transcription Regulation:

Cis-Site Seeker: Binding sites for regulatory proteins
E. Coli DNA binding site
FirstEF: First-exon & promoter prediction for human DNA
Fly Enhancer: search engine to find clusters of binding sites
NeuralNet promoter perdiction:
Promotor Scan:    Promoter regions based on scoring homologies with putative eukaryotic

Pol II promoter sequences
Tfsearch:   Searching Transcription Factor Binding Sites

Protein 3D Structure / Modelling:

PDB Viewer: Protein structure database

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
mass spectrometry

Primer Design:

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

RNA Secondary Structure Prediction:

RNA 2 Structure:    Predict RNA secondary structure
SFold: Statistical folding & rational design of nucleic acids

Molecular Modeling:

CMM:   Center for molecular modelling at NIH

Transcriptional Profiling:

Go to Microarrays & differential display page

Free Softwares:

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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