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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 protein sequence(s): tsw:opsd_human Minimum number of elements per fingerprint [2]: Maximum number of elements per fingerprint [20]: Output file [opsd_human.pscan]: |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-sequence] seqall Protein sequence(s) filename and optional
format, or reference (input USA)
-emin integer [2] Minimum number of elements per
fingerprint (Integer from 1 to 20)
-emax integer [20] Maximum number of elements per
fingerprint (Integer up to 20)
[-outfile] outfile [*.pscan] Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outfile" associated qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Protein sequence(s) filename and optional format, or reference (input 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 | <*>.pscan |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
ID OPSD_HUMAN Reviewed; 348 AA.
AC P08100; Q16414; Q2M249;
DT 01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1988, sequence version 1.
DT 20-MAR-2007, entry version 91.
DE Rhodopsin (Opsin-2).
GN Name=RHO; Synonyms=OPN2;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX MEDLINE=84272729; PubMed=6589631;
RA Nathans J., Hogness D.S.;
RT "Isolation and nucleotide sequence of the gene encoding human
RT rhodopsin.";
RL Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
RA Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
RT "Genome-wide discovery and analysis of human seven transmembrane helix
RT receptor genes.";
RL Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Retina;
RG The German cDNA consortium;
RL Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
RX PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
RA Bennett J., Beller B., Sun D., Kariko K.;
RT "Sequence analysis of the 5.34-kb 5' flanking region of the human
RT rhodopsin-encoding gene.";
RL Gene 167:317-320(1995).
RN [6]
RP REVIEW ON RP4 VARIANTS.
RX MEDLINE=94004905; PubMed=8401533;
RA Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
RA Bhattacharya S.;
[Part of this file has been deleted for brevity]
FT /FTId=VAR_004816.
FT VARIANT 209 209 V -> M (effect not known).
FT /FTId=VAR_004817.
FT VARIANT 211 211 H -> P (in RP4).
FT /FTId=VAR_004818.
FT VARIANT 211 211 H -> R (in RP4).
FT /FTId=VAR_004819.
FT VARIANT 216 216 M -> K (in RP4).
FT /FTId=VAR_004820.
FT VARIANT 220 220 F -> C (in RP4).
FT /FTId=VAR_004821.
FT VARIANT 222 222 C -> R (in RP4).
FT /FTId=VAR_004822.
FT VARIANT 255 255 Missing (in RP4).
FT /FTId=VAR_004823.
FT VARIANT 264 264 Missing (in RP4).
FT /FTId=VAR_004824.
FT VARIANT 267 267 P -> L (in RP4).
FT /FTId=VAR_004825.
FT VARIANT 267 267 P -> R (in RP4).
FT /FTId=VAR_004826.
FT VARIANT 292 292 A -> E (in CSNBAD1).
FT /FTId=VAR_004827.
FT VARIANT 296 296 K -> E (in RP4).
FT /FTId=VAR_004828.
FT VARIANT 297 297 S -> R (in RP4).
FT /FTId=VAR_004829.
FT VARIANT 342 342 T -> M (in RP4).
FT /FTId=VAR_004830.
FT VARIANT 345 345 V -> L (in RP4).
FT /FTId=VAR_004831.
FT VARIANT 345 345 V -> M (in RP4).
FT /FTId=VAR_004832.
FT VARIANT 347 347 P -> A (in RP4).
FT /FTId=VAR_004833.
FT VARIANT 347 347 P -> L (in RP4; common variant).
FT /FTId=VAR_004834.
FT VARIANT 347 347 P -> Q (in RP4).
FT /FTId=VAR_004835.
FT VARIANT 347 347 P -> R (in RP4).
FT /FTId=VAR_004836.
FT VARIANT 347 347 P -> S (in RP4).
FT /FTId=VAR_004837.
SQ SEQUENCE 348 AA; 38893 MW; 6F4F6FCBA34265B2 CRC64;
MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
//
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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
CLASS 3
Not all elements match but those that do are in order
CLASS 4
Remaining partial matches
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The program reports hits in four classes.
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 |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| fuzzpro | Protein pattern search |
| fuzztran | Protein pattern search after translation |
| helixturnhelix | Report nucleic acid binding motifs |
| oddcomp | Find 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 |