perl regular expression

[vivien]

Hallo .Iam new to perl programming but working on it.currently iam working with gene family in a particular plant..i wish to identify  sequences with the following motifs QLRDLAYDAEDCLDEFxYxx and KxWLxELRELAYDAEDCIDEF where x is any nucleotide from a plant genome....is it possible to design  a regular expression using those patterns then use it to extract  other sequences with same motifs from genome database?can somebody help formulate a regular expression using those motifs?Thanks.

[Steve Mount]

Vivien,

Those are amino acid sequences. You can indeed design a perl script to find such occurrences in protein fasta sequences, and I think that what you learn in the course  is probably sufficient for that task.

However, you really want to use more appropriate methods for this (you don't want to miss a case because of a single conservative amino acid change). 

blastp first, tblastn vs. plant genomes and hmmer (http://hmmer.janelia.org/) would be my recommendations.  You will find many genes with imperfect matches that I suspect are of interest to you, and you can easily scan the blast output for the few perfect matches that the regular expression search would have yielded.

Steve Mount

On Thu, Sep 12, 2013 at 10:34 PM, vivien <chev...@gmail.com> wrote:

Hallo .Iam new to perl programming but working on it.currently iam working with gene family in a particular plant..i wish to identify  sequences with the following motifs QLRDLAYDAEDCLDEFxYxx and KxWLxELRELAYDAEDCIDEF where x is any nucleotide from a plant genome....is it possible to design  a regular expression using those patterns then use it to extract  other sequences with same motifs from genome database?can somebody help formulate a regular expression using those motifs?Thanks.

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[RENATO AUGUSTO CORREA DOS SANTOS]

Dear both,

In the case of HMMER, they usually use an alignment of proteins to build a hmm, and with this you can search in a protein database. However, there are other tools being developed which aim to search with these protein alignment against nucleotide sequences, using similar approaches.

Best,

Renato A. C. Santos

Renato Augusto Corrêa dos Santos (Undergraduate Researcher)

Bioethanol Science and Technology Laboratory (ABTLuS-CNPEM)

+55 19 9722 5665

[chebii vivien]

Thanks for the suggestion

On 9/13/13, Steve Mount <st...@stevemount.info> wrote:
> Vivien,
>
> Those are amino acid sequences. You can indeed design a perl script to find
> such occurrences in protein fasta sequences, and I think that what you

> learn in the course <http://korflab.ucdavis.edu/unix_and_Perl/> is

> probably sufficient for that task.
>
> However, you really want to use more appropriate methods for this (you
> don't want to miss a case because of a single conservative amino acid
> change).

> blastp<http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome>first,
> tblastn<http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&BLAST_PROGRAMS=tblastn&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=&LINK_LOC=blasttab&LAST_PAGE=blastp>vs.

Vivien Jepchirchir Chebii,
Msc Bioinformatics,
Fujian Agriculture and Forestry University,
China.
Skype:Vivienne c chichi2
Phone:+8615705900460

[Steve Mount]

Renato,

You're right that being able to search nucleotide sequences with an hmm would be useful.  

This is what is on the hmmer site (the last sentence deals with searching nucleotide sequences):

The following HMMER algorithms/programs are supported by this server:

• phmmer - used to search one or more query protein sequences against a protein sequence database.

• hmmscan - search protein sequences against collections of profiles, e.g. Pfam. In HMMER2 this was called hmmpfam.

• hmmsearch - used to search one or more profiles against a protein sequence database.

• jackhmmer - iteratively search a query protein sequence, multiple sequence alignment or profile HMM against the target protein sequence database.

Longer term, we will support nhmmer that will enable searches with nucleotide sequences. This software has been released as part of the HMMER software package (version 3.1).

Vivien,

You will note that phmmer does allow searching with a single protein sequence. Also, tblastn allows you to search nucleotide sequences with a protein query (using blast rather than hmmer). 

Getting back to your original question, whatever you use, you would be able to use regular expressions to look for exact matches in the output.

Steve

[chebii vivien]

Thanks alot for your contributins...but for the problem in question
some people had done it before using the BLAST methods and also HMM
profiles obtained from Pfam((they used Pfam HMM profiles to scan
various protein databases to identify this gene family)...whetever
they got tend to have many false postives ..hence looking for a
different approach but which is more stringten......okay was thinking
probably i can build HMM profiles using manual curated gene family
sequences of this the gene family in question which are about 12.
with help of HMMER package and then validate by RBH ....but not sure
if it actually it will make sense...because i understand quality
multiple sequence alignment is fundamental for generation of quality
profiles..but with 12 closely related genes iam afraid i may not get
good results....

On 9/15/13, Steve Mount <st...@stevemount.info> wrote:
> Renato,
>
> You're right that being able to search nucleotide sequences with an hmm
> would be useful.

> This is what is on the hmmer site <http://hmmer.janelia.org/help/algo> (the

> last sentence deals with searching nucleotide sequences):
>

> The following HMMER *algorithms/programs* are supported by this server:
>>
>> - *phmmer <http://hmmer.janelia.org/search/phmmer>* - used to search

>> one or more query protein sequences against a protein sequence
>> database.
>>
>>

>> - *hmmscan <http://hmmer.janelia.org/search/hmmscan>* - search protein
>> sequences against collections of profiles, *e.g.* Pfam. In HMMER2 this
>> was called *hmmpfam*.
>>
>>
>> - *hmmsearch <http://hmmer.janelia.org/search/hmmsearch>* - used to

>> search one or more profiles against a protein sequence database.
>>
>>

>> - *jackhmmer <http://hmmer.janelia.org/search/jackhmmer>* -

>> iteratively search a query protein sequence, multiple sequence
>> alignment or
>> profile HMM against the target protein sequence database.
>>

>> Longer term, we will support *nhmmer* that will enable searches with

>> nucleotide sequences. This software has been released as part of the
>> HMMER

>> software package <http://hmmer.janelia.org/software> (version 3.1).

>
>
> Vivien,
>
> You will note that phmmer does allow searching with a single protein
> sequence. Also, tblastn allows you to search nucleotide sequences with a
> protein query (using blast rather than hmmer).
> Getting back to your original question, whatever you use, you would be able
> to use regular expressions to look for exact matches in the output.
>
> Steve
>
>
>
>
>
> On Sat, Sep 14, 2013 at 8:33 AM, RENATO AUGUSTO CORREA DOS SANTOS <
> rcs....@ig.com.br> wrote:
>
>> Dear both,
>>
>> In the case of HMMER, they usually use an alignment of proteins to build
>> a
>> hmm, and with this you can search in a protein database. However, there
>> are
>> other tools being developed which aim to search with these protein
>> alignment against nucleotide sequences, using similar approaches.
>>
>> Best,
>>
>> Renato A. C. Santos
>>
>>
>> On Fri, Sep 13, 2013 at 7:17 AM, Steve Mount
>> <st...@stevemount.info>wrote:
>>
>>> Vivien,
>>>
>>> Those are amino acid sequences. You can indeed design a perl script to
>>> find such occurrences in protein fasta sequences, and I think that what
>>> you

>>> learn in the course <http://korflab.ucdavis.edu/unix_and_Perl/> is

>>> probably sufficient for that task.
>>>
>>> However, you really want to use more appropriate methods for this (you
>>> don't want to miss a case because of a single conservative amino acid
>>> change).

>>> blastp<http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome>first,
>>> tblastn<http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&BLAST_PROGRAMS=tblastn&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=&LINK_LOC=blasttab&LAST_PAGE=blastp>vs.

>> *Renato Augusto Corrêa dos Santos (Undergraduate Researcher)*

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[RENATO AUGUSTO CORREA DOS SANTOS]

Dear Steve,

Thank you so much.

I still did not work with nucleotide search (only with protein alignment agains prot db).

I actually want to understand the process. Is it possible to search a nucl database with a protein alignment?

I also agree with Vivien: better is the alignment, better will be the results! :-)

Best regards, thank you so much for your reply.

Renato.

[Steve Mount]

Renato,

I don't think that there is any way to search a nucleotide database with a protein "alignment" (actually, a PSSM or HMM derived from an alignment). However, you can search a nucleotide database with a single protein sequence (tblastn) and you can, of course, search a protein database with profile (using Psi-blast or HMMer).

Steve Mount

[RENATO AUGUSTO CORREA DOS SANTOS]

Sure, thanks.

I would say "profile", not alignment.
Best,

Renato.