Protein analysis
General purpose
- PredictProtein
- Alignment
- Pattern search
- Protein pattern search (Fuzzpro)
- Look for all the sequences containing a given pattern (Patmatdb)
- Look for all the pattern on a given protein seq (Patmatmotifs)
- Convention to write a pattern in EMBOSS
- Profile search
- Look for the all the sequences containing a given profile (Profit)
- Creates matrices/profiles from multiple alignments (Prophecy)
- Find matches of a profile and a sequence(gapped alignment - Prophet)
- Scan proteins using Prints db (pscan)
- HMM search
- Look for all the pfam models on a given sequence (Pfam
search)
- If you know the accession of a SwissProt/Trembl sequence, use the
precomputed Swissfam
Special features
Discovering pattern or motifs
- Pratt: A pattern
discovery tool
- Spratt, Spratt2: Structure motif
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