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pscan |
Fingerprints are groups of conserved motifs or elements that together form a diagnostic signature for particular protein families.
An uncharacterised sequence matching all motifs or elements can then be readily diagnosed as a true match to a particular family fingerprint.
They can be used to diagnose family relationships in newly-determined sequences (especially from genome projects).
Usually the motifs or elements do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.
Diagnostically, this is more powerful than using single motifs by virtue of the biological context afforded by matching motif neighbours.
pscan finds matches between a query protein sequence and the motifs or elements in the PRINTS database. It reports various classes of matches:
The home web page of the PRINTS database is: http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/
% pscan Scans proteins using PRINTS Input sequence(s): sw:OPSD_HUMAN Minimum number of elements per fingerprint [2]: Maximum number of elements per fingerprint [20]: Output file [opsd_human.pscan]: %
Mandatory qualifiers: [-sequence] seqall Sequence database USA -emin integer Minimum number of elements per fingerprint -emax integer Maximum number of elements per fingerprint [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-emin | Minimum number of elements per fingerprint | Integer from 1 to 20 | 2 |
-emax | Maximum number of elements per fingerprint | Integer up to 20 | 20 |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.pscan |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
CLASS 1 Fingerprints with all elements in order Fingerprint GPCRRHODOPSN Elements 7 Accession number PR00237 Rhodopsin-like GPCR superfamily signature Element 1 Threshold 54% Score 64% Start position 39 Length 25 Element 2 Threshold 49% Score 75% Start position 72 Length 22 Element 3 Threshold 48% Score 56% Start position 117 Length 23 Element 4 Threshold 50% Score 69% Start position 152 Length 22 Element 5 Threshold 51% Score 74% Start position 204 Length 24 Element 6 Threshold 42% Score 75% Start position 250 Length 25 Element 7 Threshold 46% Score 67% Start position 288 Length 27 CLASS 2 All elements match but not all in the correct order Fingerprint RHODOPSIN Elements 6 Accession number PR00579 Rhodopsin signature Element 1 Threshold 80% Score 96% Start position 3 Length 19 Element 2 Threshold 76% Score 100% Start position 22 Length 17 Element 3 Threshold 53% Score 92% Start position 85 Length 17 Element 4 Threshold 71% Score 100% Start position 191 Length 17 Element 5 Threshold 56% Score 99% Start position 271 Length 19 Element 6 Threshold 81% Score 93% Start position 319 Length 14 CLASS 3 Not all elements match but those that do are in order Fingerprint PROFILIN Elements 6 Accession number PR00392 Profilin signature Element 6 Threshold 31% Score 31% Start position 18 Length 18 Element 6 Threshold 37% Score 37% Start position 318 Length 15 CLASS 4 Remaining partial matches Fingerprint NANEUSMPORT Elements 8 Accession number PR00176 Sodium/chloride neurotransmitter symporter signature Element 2 Threshold 47% Score 47% Start position 38 Length 20
The data files must have been created before running this program. This is done by running the printsextract program with the "prints.dat" file from a PRINTS release. You may have to ask your system manager to do this.
"prints.mat file not found. Create it with printsextract."
then your local PRINTS data has not been set up correctly in your EMBOSS DATA directory. Use 'printsextract' to do this.
Program name | Description |
---|---|
antigenic | Finds antigenic sites in proteins |
digest | Protein proteolytic enzyme or reagent cleavage digest |
fuzzpro | Protein pattern search |
fuzztran | Protein pattern search after translation |
helixturnhelix | Report nucleic acid binding motifs |
oddcomp | Finds protein sequence regions with a biased composition |
patmatdb | Search a protein sequence with a motif |
patmatmotifs | Search a PROSITE motif database with a protein sequence |
pepcoil | Predicts coiled coil regions |
preg | Regular expression search of a protein sequence |
sigcleave | Reports protein signal cleavage sites |