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 the Whitehead Institute
- RepeatMasker: screen DNA sequences against a library of repetitive elements
- Bankit!: GenBank sequence submissions (NCBI)
Searching for similar sequences (BLAST, etc.)
- NCBI BLAST: use the Basic Local Alignment Search Tool to search NCBI databases
- BLAST nucleotide sequences (BCM)
- Ensembl BLASTView: search any of the Ensembl genome projects
- BLAST against a variety of species (Sanger Institute)
Pairwise alignment
- Baylor College of Medicine: SIM, BLAST, LAP2, PGWISE, PCWISE
- SIM4: to align cDNA and genomic DNA
- GeneWise (Wise2): align DNA to protein
- Michigan Tech: global alignment (GAP) and local alignment (SIM)
- FASTA programs for a variety of alignment options
- BLAST 2 sequences: local alignmnent with BLAST
- LALIGN: local alignment at the University of Virginia
- Dotlet: sequence comparisons using a dot matrix
- Nucleic acid dot plots: a different dot matrix implementation
- Smith-Waterman: optimal local alignment (MPsrch from EMBL-EBI)
- 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]
- MAP (Multiple Alignment Program) at Baylor College of Medicine
- PRALINE: "with many options to optimise the information for each of the input sequences"
- Multalin: "Multiple sequence alignment with hierarchical clustering" at INRA
- Parallel PRRN: "Multiple sequence alignment by the best-first iterative refinement strategy with tree-dependent partitioning"
- 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
- TRANSFAC (transcription factor database), including MATCH and PATCH search tools [Whitehead only: use you BaRC account username and password]
- MEME and MAST: "biological sequence motif discovery tool" and "Motif Alignment and Search Tool"
- Regulatory Sequence Analysis Tools: detect regulatory signals in non-coding sequences (SCMBB, Belgium)
- EMBOSS: dreg, fuzznuc, tfscan
- Gene Feature Searches (BCM)
- Frame - ProfileScan: Search a short DNA sequence against a protein profile database
- TESS: Transcription Element Search System
- Signal Scan: find homologies of published signal sequences
- MatInspector (Genomatix): "fast and versatile tool for detection of consensus matches in nucleotide sequence data"
- ModelInspector (Genomatix): generate sequence models
- PatScan: search protein or DNA sequence databases for a pattern (ANL)
Gene finding
- BCM Gene Finder: FGENES, FGENESH, BESTORF, SPL, and many other programs
- GenomeScan
- GENSCAN
- Gene Finder: Michael Zhang (CSHL)
- Softberry Gene Finder: many tools
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 NIH
- EMBOSS GUI at the Whitehead Institute [Whitehead only]
- The Sequence Manipulation Suite
- CMS Molecular Biology Resource at the San Diego Supercomputer Center (SDSC)
- ABIM list of analysis tools: Atelier BioInformatique at Université Aix-Marseille
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"
- GeneDoc: "a full featured multiple sequence alignment editor, analyser and shading utility for Windows"
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| Last Updated: January 06 2006 10:41:24 am | ||