Sequence utilities
- Convert a sequence (with readseq): change DNA/protein sequence to almost any format
- Shuffle a sequence: randomize a DNA/protein sequence to use as a statistical control
- Clean a sequence: remove numbers, spaces, and other non-sequence characters
- Reverse Complement
- ORF finder from NCBI
- Six frame translation
- Restriction enzyme analysis (with WebCutter): generate a map of enzyme sites
- VecScreen: "a system for quickly identifying segments of a nucleic acid sequence that may be of vector origin"
- Generate primers (with Primer3) at Whitehead Institute
- RepeatMasker: screen DNA sequences against a library of repetitive elements
Searching for similar sequences (BLAST, etc.)
- NCBI BLAST: use the Basic Local Alignment Search Tool to search NCBI databases
- Ensembl BLASTView: search any of the Ensembl genome projects
- BLAST against a variety of species (Sanger Institute)
Pairwise alignment
- SIM4: to align cDNA and genomic DNA
- GeneWise (Wise2): align DNA to protein
- FASTA programs for a variety of alignment options
- BLAST 2 sequences: local alignmnent with BLAST
- LALIGN: local alignment at EMBNET
- Dotlet: sequence comparisons using a dot matrix
- Nucleic acid dot plots: a different dot matrix implementation
- Smith-Waterman: optimal local alignment using EMBOSS's "water" (defaults: Gap opening penalty = 10; Gap extension penalty = 0.5)
Multiple sequence alignment
- ClustalW at EMBL-EBI [download ClustalX]
- PRALINE: "with many options to optimise the information for each of the input sequences"
- WebLogo sequence logo generation form: generate a "sequence logo" image of a multiple sequence alignment
- WebLogo: a sequence logo generator
- NJplot: software to generate a phylogenetic tree from ClustalX output
Pattern searching
- MEME and MAST: "biological sequence motif discovery tool" and "Motif Alignment and Search Tool"
- EMBOSS: dreg, fuzznuc, tfscan
Portals for comprehensive analysis
- ExPASy: "Expert Protein Analysis System" of the Swiss Institute of Bioinformatics [US mirror]
- EBI Database Searching, Browsing and Analysis Tools
- EMBOSS GUI at the Whitehead Institute [Whitehead only]
Software for nucleic acid sequence analysis and bioinformatics (downloads and help)
- EMBOSS: a package of free software for sequence analysis; on WIBR BaRC system.
- BioPerl: Perl modules designed to handle common bioinformatics tasks
- RasMol and Chime: "software for looking at macromolecular structure and its relation to function"
| Bioinformatics and Research Computing | Whitehead Institute for Biomedical Research | |
| Last Updated: June 23 2010 10:42:05 am | ||