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Search with a protein sequence against Pfam library
OVERVIEW
Pfam [1] is a large collection of protein families and domains. The database contains
multiple sequence alignments and hidden Markov models covering many common
protein domains of these families. To search against Pfam database the program
hmmscan [2,
3] is used.
Hmmscan calculates the matching score between the query sequence and each
domain found in Pfam library in bit score and in E-value. In this service the cut-off
threshould should be given as E-value. Found motifs with smaller E-value than the
threshould value are lited. Smaller cut-off E-value makes the search more selective.
RESULTS
The found motifs are listed in a table. From the ID numbers of Pfam you can jump into
DBGET to look at the hits as well as related informations precisely. Under Position (E-value)
column of the table the position (start and end sequence numbers) and
the scores of found motifs are listed. Click Detail bottun to see actual
positions of the motif along the query sequence . (shown in red)
You can search your query sequnce against a profile library defined by a user which contains
either single or multiple profile data in HMMER save file format.
Check the "User-defined
Profile Library" box in the motif library list and provide a file name containing the
profile.
The user defined profile library may be a subset of original Pfam database or one generated from multiple sequence alignment data.
References
-
1.
Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy SR.,
Griffiths-Jones S., Howe K.L., Marshall M. and Sonnhammer E.L.
"The Pfam Protein Families Database"
Nucl. Acids Res. 30(1):276-280, 2002.
-
2.
Eddy S.R.
Profile hidden Markov models
Bioinformatics 14:755-763 (1998)
-
3. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids."
Durbin R., Eddy S., Krogh A., Mitchison G., Cambridge University Press (1998) 350 pages.