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Sequence, Structure & Function Analysis
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
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
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
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

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
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:

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 
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:

Cis-Site Seeker: Binding sites for regulatory proteins
Cister:  Cis-element Cluster Finder
E. Coli DNA binding site
Eponine: Tool to detect mammalian transcription start sites
FirstEF: First-exon & promoter prediction for human DNA
Fly Enhancer: search engine to find clusters of 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
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
mass spectrometry
Prowl:   Software for protein mass spectrometry

Protein Splicing:

InBase:   Inteins in sequenced genes

Primer Design:

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
 

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
 
Molecular Modeling:
 
CMM:   Center for molecular modelling at NIH

Alternate Splicing Analysis:

ASAP: Alternate splicing analysis tool at UCLA

Transcriptional Profiling:

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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