[Bioperl-l] Bioperl-l Digest, Vol 106, Issue 18

Michael Coyne mcoyne at channing.harvard.edu
Thu Feb 23 21:01:51 EST 2012


Sixty is evenly divisible by three (20 codons), while 70 is not...?

On Thu, Feb 23, 2012 at 12:00 PM, <bioperl-l-request at lists.open-bio.org>wrote:

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> Today's Topics:
>
>   1.  Fasta sequence width question ( Francisco J. Ossand?n )
>   2. Re:  Fasta sequence width question (Brian Osborne)
>   3. Re:  Fasta sequence width question ( Francisco J. Ossand?n )
>   4. Re:  Fasta sequence width question (Chris Fields)
>   5. Re:  Fasta sequence width question (Brian Osborne)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 22 Feb 2012 15:55:23 -0300
> From: " Francisco J. Ossand?n " <fossandonc at hotmail.com>
> Subject: [Bioperl-l] Fasta sequence width question
> To: <Bioperl-l at lists.open-bio.org>
> Message-ID: <BLU0-SMTP225B3D87620D5BC0691B940CF640 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
> I have a question about the width used by Bioperl in the Fasta format. This
> format recommends that lines of text be shorter than 80 characters, but
> there is no really fixed length for the sequence lines.
> http://en.wikipedia.org/wiki/FASTA_format
> http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
>
> I usually download sequences from NCBI and their Fasta sequences always use
> a sequence line width of 70 characters (like
> http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while Bioperl
> uses a default of 60 to write in Fasta format using Bio::SeqIO::Fasta
> ("BEGIN { $WIDTH = 60}"). Is there a particular reason to set the width at
> 60 characters?? Or maybe it could be changed to 70 to match NCBI??
>
> Cheers,
>
> Francisco J. Ossandon
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 22 Feb 2012 14:28:12 -0500
> From: Brian Osborne <bosborne11 at verizon.net>
> Subject: Re: [Bioperl-l] Fasta sequence width question
> To: Francisco J. Ossand?n <fossandonc at hotmail.com>
> Cc: Bioperl-l at lists.open-bio.org
> Message-ID: <871478E1-15CD-4F3D-B95E-71193723D593 at verizon.net>
> Content-Type: text/plain; charset=iso-8859-1
>
> Francis,
>
> You can set this yourself.
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width
>
> Brian O.
>
>
> On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:
>
> > Hello,
> > I have a question about the width used by Bioperl in the Fasta format.
> This
> > format recommends that lines of text be shorter than 80 characters, but
> > there is no really fixed length for the sequence lines.
> > http://en.wikipedia.org/wiki/FASTA_format
> > http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
> >
> > I usually download sequences from NCBI and their Fasta sequences always
> use
> > a sequence line width of 70 characters (like
> > http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while
> Bioperl
> > uses a default of 60 to write in Fasta format using Bio::SeqIO::Fasta
> > ("BEGIN { $WIDTH = 60}"). Is there a particular reason to set the width
> at
> > 60 characters?? Or maybe it could be changed to 70 to match NCBI??
> >
> > Cheers,
> >
> > Francisco J. Ossandon
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 22 Feb 2012 18:37:42 -0300
> From: " Francisco J. Ossand?n " <fossandonc at hotmail.com>
> Subject: Re: [Bioperl-l] Fasta sequence width question
> To: "'Brian Osborne'" <bosborne11 at verizon.net>
> Cc: Bioperl-l at lists.open-bio.org
> Message-ID: <BLU0-SMTP324801F8A32A12FE1700ED0CF640 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Yes, I know about the method to change the width myself, thanks. =)
> My question was more about if there was an specific reason to choose that
> default value (60) instead of the NCBI value (70). And if it should be
> changed to 70 to match NCBI or not.
>
> Cheers,
>
> Francisco J. Ossandon
>
> -----Mensaje original-----
> De: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Brian Osborne
> Enviado el: mi?rcoles, 22 de febrero de 2012 16:28
> Para: Francisco J. Ossand?n
> CC: Bioperl-l at lists.open-bio.org
> Asunto: Re: [Bioperl-l] Fasta sequence width question
>
> Francis,
>
> You can set this yourself.
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width
>
> Brian O.
>
>
> On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:
>
> > Hello,
> > I have a question about the width used by Bioperl in the Fasta format.
> > This format recommends that lines of text be shorter than 80
> > characters, but there is no really fixed length for the sequence lines.
> > http://en.wikipedia.org/wiki/FASTA_format
> > http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
> >
> > I usually download sequences from NCBI and their Fasta sequences
> > always use a sequence line width of 70 characters (like
> > http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while
> > Bioperl uses a default of 60 to write in Fasta format using
> > Bio::SeqIO::Fasta ("BEGIN { $WIDTH = 60}"). Is there a particular
> > reason to set the width at
> > 60 characters?? Or maybe it could be changed to 70 to match NCBI??
> >
> > Cheers,
> >
> > Francisco J. Ossandon
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 22 Feb 2012 16:42:04 -0600
> From: Chris Fields <cjfields at illinois.edu>
> Subject: Re: [Bioperl-l] Fasta sequence width question
> To: bioperl-l at lists.open-bio.org
> Message-ID: <4F456F3C.4070903 at illinois.edu>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
> No reason, beyond legacy and possibly a fear that changing it could
> cause unforeseen consequences down the road.
>
> chris
>
> On 02/22/2012 03:37 PM, Francisco J. Ossand?n wrote:
> > Yes, I know about the method to change the width myself, thanks. =)
> > My question was more about if there was an specific reason to choose that
> > default value (60) instead of the NCBI value (70). And if it should be
> > changed to 70 to match NCBI or not.
> >
> > Cheers,
> >
> > Francisco J. Ossandon
> >
> > -----Mensaje original-----
> > De: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Brian Osborne
> > Enviado el: mi?rcoles, 22 de febrero de 2012 16:28
> > Para: Francisco J. Ossand?n
> > CC: Bioperl-l at lists.open-bio.org
> > Asunto: Re: [Bioperl-l] Fasta sequence width question
> >
> > Francis,
> >
> > You can set this yourself.
> >
> >
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width
> >
> > Brian O.
> >
> >
> > On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:
> >
> >> Hello,
> >> I have a question about the width used by Bioperl in the Fasta format.
> >> This format recommends that lines of text be shorter than 80
> >> characters, but there is no really fixed length for the sequence lines.
> >> http://en.wikipedia.org/wiki/FASTA_format
> >> http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
> >>
> >> I usually download sequences from NCBI and their Fasta sequences
> >> always use a sequence line width of 70 characters (like
> >> http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while
> >> Bioperl uses a default of 60 to write in Fasta format using
> >> Bio::SeqIO::Fasta ("BEGIN { $WIDTH = 60}"). Is there a particular
> >> reason to set the width at
> >> 60 characters?? Or maybe it could be changed to 70 to match NCBI??
> >>
> >> Cheers,
> >>
> >> Francisco J. Ossandon
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 22 Feb 2012 16:50:58 -0500
> From: Brian Osborne <bosborne11 at verizon.net>
> Subject: Re: [Bioperl-l] Fasta sequence width question
> To: Francisco J. Ossand?n <fossandonc at hotmail.com>
> Cc: Bioperl-l at lists.open-bio.org
> Message-ID: <9A106184-4082-4E23-B91B-6DBCCE0B319E at verizon.net>
> Content-Type: text/plain; charset=iso-8859-1
>
> Francis,
>
> There's has never been a decision, to my knowledge, to base "global"
> Bioperl defaults on NCBI's conventions. Yes, there are tools in Bioperl
> that access NCBI in various ways but Bioperl does not generally refer to
> NCBI for its definitions.
>
> Brian O.
>
> On Feb 22, 2012, at 4:37 PM, Francisco J. Ossand?n wrote:
>
> > Yes, I know about the method to change the width myself, thanks. =)
> > My question was more about if there was an specific reason to choose that
> > default value (60) instead of the NCBI value (70). And if it should be
> > changed to 70 to match NCBI or not.
> >
> > Cheers,
> >
> > Francisco J. Ossandon
> >
> > -----Mensaje original-----
> > De: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Brian Osborne
> > Enviado el: mi?rcoles, 22 de febrero de 2012 16:28
> > Para: Francisco J. Ossand?n
> > CC: Bioperl-l at lists.open-bio.org
> > Asunto: Re: [Bioperl-l] Fasta sequence width question
> >
> > Francis,
> >
> > You can set this yourself.
> >
> >
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width
> >
> > Brian O.
> >
> >
> > On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:
> >
> >> Hello,
> >> I have a question about the width used by Bioperl in the Fasta format.
> >> This format recommends that lines of text be shorter than 80
> >> characters, but there is no really fixed length for the sequence lines.
> >> http://en.wikipedia.org/wiki/FASTA_format
> >> http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
> >>
> >> I usually download sequences from NCBI and their Fasta sequences
> >> always use a sequence line width of 70 characters (like
> >> http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while
> >> Bioperl uses a default of 60 to write in Fasta format using
> >> Bio::SeqIO::Fasta ("BEGIN { $WIDTH = 60}"). Is there a particular
> >> reason to set the width at
> >> 60 characters?? Or maybe it could be changed to 70 to match NCBI??
> >>
> >> Cheers,
> >>
> >> Francisco J. Ossandon
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> End of Bioperl-l Digest, Vol 106, Issue 18
> ******************************************
>


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