Protein Sequence Tools
- AASTATS - Statistics Based on Amino Acid Abundance (replaced by PEPINFO)
- ALIGN - Optimal Global Alignment of Two PS
- BL2SEQ - Compare proteins to each other with BLAST
- BL2SEQX Compare a protein to a nucleotide sequence with BLAST, use BL2SEQ
- BLASTP - Compare a PS to a PS DB
- BLIMPS - Sequence Search Against BLOCKS Profiles
- CHOFAS - Predict Secondary Stucture of PS(s) (replaced by PROTEUS)
- CLUSTALW - Multiple Sequence Alignment
- CLUSTALWPROF - Align Sequences to Existing Alignment (Profile)
- DEGAPSEQ - Remove Gaps from Sequences
- EXTCOEF - Extinction coefficient calculation (replaced by PEPSTATS)
- FASTA - Heuristic Sequence Similarity Search (PS Or DB)
- FingerPRINTScan - PRINTS fingerprint identification
- GOR4 - Predict Secondary Structure of PS (replaced by PROTEUS)
- GREASE - Kyte-Doolittle Hydropathy Profile (replaced by PEPWINDOW).
- HMMPFAM - Search against Pfam HMM database
- HELIXTURNHELIX (HTH) - Predict HTH Motifs in Protein Chains
- LALIGN - Calculate N-Best Local PS Alignments
- MSA - Multiple Sequence Alignment (Sum-of-Pairs Criterion)
- PEPINFO - histograms of protein properties
- PEPSTATS - extinction coefficient, PI calculation, etc.
- PEPWINDOW - Protein hydropathy plots (Replaces Grease).
- PFSCAN- Sequence search against a set of profiles
- PFSEARCH - Search a PROSITE profile against a sequence database
- PI - Isoelectric point determination (replaced by PEPSTATS)
- PPSEARCH - Search Prosite DB for Patterns in a PS
- PROSEARCH - Search Prosite DB for Patterns in a PS
- PROTEUS - Protein Secondary Structure prediction
(replaces CHOFAS, GOR4) - PRSS - Compare a PS to a Shuffled PS
- PSIBLAST - Position Specific Iterative BLAST
- RPSBLAST - Compare a PS to a Conserved Domain DB
- SAPS - Statistical Analysis of PS (replaced by PEPSTATS)
- SSEARCH - Smith-Waterman Local Alignment of Proteins
- TBLASTN - Compare a PS to a translated DB
- TFASTA - Compare a PS to a NS->PSDB
- TFASTX - Comp PS to Trans DNA (NS Or DB)
- TFASTY - Comp PS to Trans DNA (NS Or DB)
- TMAP - Prediction of Transmembrane Segments
- TMHMM - Predict location of transmembrane helices and location of intervening loop regions
If you don't see the tool you need, please Let us know! We can add tools very quickly.
