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pcr_seq
pcr_seq runs virtual PCR on all sequences in the stream given a forward and a reverse primer pattern. pcr_seq uses scan_for_matches as pattern search engine. Ambiguity codes can be used in the primer sequences as well as mismatches, insertions, and deletions can be allowed by appending this information like this:
ATCGCAGTCA[3,2,1]
Which allows 3 mismatches, 2 deletions, and 1 insertion. Other more fine grained patterns can be used. Consult the documentation for scan_for_matches (see below).
pcr_seq checks all primer pattern combinations and possible PCR products will have a TYPE key that indicates
what primers gave rise to the product.
scan_for_matches needs to be installed for pcr_seq to work:
http://blog.theseed.org/servers/2010/07/scan-for-matches.html
... | pcr_seq [options]
[-? | --help] # Print full usage description.
[-f <string> | --forward=<string>] # Forward adaptor (5'-3').
[-F <string> | --forward_rc=<string>] # Forward adaptor (3'-5').
[-r <string> | --reverse=<string>] # Reverse adaptor (3'-5').
[-R <string> | --reverse_rc=<string>] # Reverse adaptor (5'-3').
[-m <uint> | --max_dist=<uint>] # Maximum distance - Default=5000
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following sequence in the file test.fna:
>test
tgCGATCGAGCTactagctagctatcatcgatctgAGTCAGTCATct
We can run virtual PCR using pcr_seq using the following primers:
Forward: 5' CGATCGAGCT 3'
Reverse: 5' ATGACTGACT 3'
read_fasta -i test.fna | pcr_seq -f CGATCGAGCT -R ATGACTGACT
SEQ_NAME: test
SEQ: tgCGATCGAGCTactagctagctatcatcgatctgAGTCAGTCATct
SEQ_LEN: 47
---
SEQ_NAME: test
SEQ: CGATCGAGCTactagctagctatcatcgatctgAGTCAGTCAT
SEQ_LEN: 43
REC_TYPE: PCR
STRAND: +
TYPE: FORWARD_REVERSE
PCR_BEG: 3
PCR_END: 45
---
Martin Asser Hansen - Copyright (C) - All rights reserved.
September 2010
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
pcr_seq is part of the Biopieces framework.