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)
- ePESTfind - Identify motifs susceptible to protease cleavage
- 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)
- MView_blast - Display blast results as a multiple alignment
- 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
- Proteus - Protein secondary structure prediction (replaces CHOFAS, GOR4)
- PRSS - Compare a PS to a shuffled PS
- PSIBLAST - Position specific iterative BLAST
- Readseq - Extract sequences and translate into new formats
- 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 transl DNA (NS Or DB)
- TFASTY - Comp PS to transl DNA (NS Or DB)
- TMAP - Prediction of transmembrane segments
If you don't see the tool you need, please Let us know! We can add tools very quickly.
