Restriction Digests with ambiguity

[sudders]

Hi All,

I'm trying to identify sites restriction sites in the genome. Some of the enzymes I'm using contain ambiguity, e.g. ApoI whose site is RAATTY.

Initially i've been trying to use oligoMatch which is part of the UCSC download. But although it claims to take ambiguity codes, and processes my genome using the RAATTY site as input, it actually outputs any sites with AATT. Which is odd because UCSC say they use oligoMatch to produce the restriction tracks they show on the browser, which are correct.

Anyone know of any other tool that will do this, or how to make oligoMatch work for me?

[RDW]

Anyone know of any other tool that will do this, or how to make oligoMatch work for me?

EMBOSS restrict?:

http://emboss.sourceforge.net/

http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/restrict.html

[sudders]

Cheers that worked great thanks.

For anyone reading this in the future though should note that our 128GB server didn't have enough memory to process the whole genome in one go and it was necessary to split it into chromosomes.

[rhinoceros]

Biopieces has digest_seq

Biopiece: digest_seq

Summary

Split sequences in the stream at a given restriction enzyme's cleavage sites.

Description

digest_seq split sequences in the stream at a given restriction
enzyme's cleavage sites. For each digestion product a new record is created and
output to the stream. digest_seq requires two arguments:

1. The restriction enzyme recognition pattern
2. Cut position relative to the above match

E.g. the common restriction enzyme BamHI recognizes the pattern GGATCC and the
cut position for this enzyme is 1 indicating that the cleavage site is after
the first G:

cut_pos 1 23456
pattern G|GATCC
^

Patterns can contain IUPAC ambiguity codes.

Records with digestion products have a REC_TYPE: DIGEST key/value pair added.
Furthermore, the sequence coordinates are appended to the sequence name in
brackets (0-based) and as S_BEG and S_END keys.

To obtain the reverse-complement products use reverse_seq and
complement_seq before digest_seq.

Usage

... | digest_seq [options]

Options

[-? | --help] # Print full usage description.
[-p <string> | --pattern=<string>] # Restriction enzyme recognition pattern.
[-c <int> | --cut_pos=<int>] # Cut position relative to pattern match.
[-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.

Examples

Consider the following sequence in the file test.fna:

>test
cgatcgatcGGATCCgagagggtgtgtagtgGAATTCcgctgc

We can digest this sequence with BamHI like this:

read_fasta -i test.fna | digest_seq -p GGATCC -c 1

SEQ_NAME: test[0-9]
SEQ: cgatcgatcG
SEQ_LEN: 10
S_BEG: 0
S_END: 9
REC_TYPE: DIGEST
---
SEQ_NAME: test[10-42]
SEQ: GATCCgagagggtgtgtagtgGAATTCcgctgc
SEQ_LEN: 33
S_BEG: 10
S_END: 42
REC_TYPE: DIGEST
---

To obtain the - strand digestion products we re-read the file and
reverse-complment the sequence before digestion like this:

read_fasta -i test.fna | reverse_seq | complement_seq | digest_seq -p GGATCC -c 1

SEQ_NAME: test[0-28]
SEQ: gcagcgGAATTCcactacacaccctctcG
SEQ_LEN: 29
S_BEG: 0
S_END: 28
REC_TYPE: DIGEST
---
SEQ_NAME: test[29-42]
SEQ: GATCCgatcgatcg
SEQ_LEN: 14
S_BEG: 29
S_END: 42
REC_TYPE: DIGEST
---

It is also possible to do restriction enzyme digestion with multipe enzymes
simply by piping the result through digest_seq multiple times. Here we
first digest with BamHI (pattern: GGATCC, cut_pos: 1) and then with EcoRI
(pattern: GAATTC, cut_pos: 1):

read_fasta -i test.fna | digest_seq -p GGATCC -c 1 | digest_seq -p GAATTC -c 1

SEQ_NAME: test[0-9][0-9]
SEQ: cgatcgatcG
SEQ_LEN: 10
S_BEG: 0
S_END: 9
REC_TYPE: DIGEST
---
SEQ_NAME: test[10-42][0-21]
SEQ: GATCCgagagggtgtgtagtgG
SEQ_LEN: 22
S_BEG: 0
S_END: 21
REC_TYPE: DIGEST
---
SEQ_NAME: test[10-42][22-32]
SEQ: AATTCcgctgc
SEQ_LEN: 11
S_BEG: 22
S_END: 32
REC_TYPE: DIGEST
---

See also

rescan_seq

read_fasta

reverse_seq

complement_seq

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

[email protected]

September 2010

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

digest_seq is part of the Biopieces framework.

http://www.biopieces.org

This is an option for RAM-limited devices.