From fungazid at yahoo.com  Mon Jan 11 09:26:34 2010
From: fungazid at yahoo.com (Fungazid)
Date: Mon, 11 Jan 2010 06:26:34 -0800 (PST)
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the ORF
	sequence
Message-ID: <480812.49255.qm@web65508.mail.ac4.yahoo.com>

Hello people,

I just installed emboss on linux ubuntu (using the ubuntu synaptic package manager). I am using the getorf program, and I see it gives me this kind of output lines:

>00001_3 [803 - 1120] 
LARLRFVVLGNSFIASAKGWSTPYGPTTFGPFRSCIYPRVFRSTRVRKAMATRIGSNRVN
ILIRCTXXXXXXXXXXXXXXXXXXXXXXXXXNPYLGWWCYIFCIFR 

I don't like the Xs as they represent unspecified amino acids. Is there an input parameter to tell the program to report only the regions before and after the Xs ?

In addition (and maybe this is beyond the scope of this mailing list) what is the biological meaning of such Xs ?


thanks,
Avi




      


From biopython at maubp.freeserve.co.uk  Mon Jan 11 10:53:02 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 11 Jan 2010 15:53:02 +0000
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the
	ORF sequence
In-Reply-To: <480812.49255.qm@web65508.mail.ac4.yahoo.com>
References: <480812.49255.qm@web65508.mail.ac4.yahoo.com>
Message-ID: <320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>

On Mon, Jan 11, 2010 at 2:26 PM, Fungazid <fungazid at yahoo.com> wrote:
>
> Hello people,
>
> I just installed emboss on linux ubuntu (using the ubuntu synaptic package manager). I am using the getorf program, and I see it gives me this kind of output lines:
>
>>00001_3 [803 - 1120]
> LARLRFVVLGNSFIASAKGWSTPYGPTTFGPFRSCIYPRVFRSTRVRKAMATRIGSNRVN
> ILIRCTXXXXXXXXXXXXXXXXXXXXXXXXXNPYLGWWCYIFCIFR
>
> I don't like the Xs as they represent unspecified amino acids. Is there an input parameter to tell the program to report only the regions before and after the Xs ?
>
> In addition (and maybe this is beyond the scope of this mailing list) what is the biological meaning of such Xs ?

What was the input sequence like? Was there a stretch of NNNNN perhaps?

Peter

From fungazid at yahoo.com  Tue Jan 12 08:33:14 2010
From: fungazid at yahoo.com (Fungazid)
Date: Tue, 12 Jan 2010 05:33:14 -0800 (PST)
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the
	ORF sequence
In-Reply-To: <320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>
References: <480812.49255.qm@web65508.mail.ac4.yahoo.com>
	<320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>
Message-ID: <488158.80632.qm@web65501.mail.ac4.yahoo.com>

Hi Peter,

The input is a simple?fasta file with only A,C,T,G letters and nothing else, so I wouldn't expect any Xs. In addition, even if there?would be?Ns (and there are no Ns) the program cannot know if such Ns do not include stop codons so it should not consider them as part of an?ORF.

Best,
Avi



----- Original Message ----
From: Peter <biopython at maubp.freeserve.co.uk>
To: Fungazid <fungazid at yahoo.com>
Cc: emboss at lists.open-bio.org
Sent: Mon, January 11, 2010 5:53:02 PM
Subject: Re: [EMBOSS] getorf includes unspecified amino acids as part of the ORF sequence

On Mon, Jan 11, 2010 at 2:26 PM, Fungazid <fungazid at yahoo.com> wrote:
>
> Hello people,
>
> I just installed emboss on linux ubuntu (using the ubuntu synaptic package manager). I am using the getorf program, and I see it gives me this kind of output lines:
>
>>00001_3 [803 - 1120]
> LARLRFVVLGNSFIASAKGWSTPYGPTTFGPFRSCIYPRVFRSTRVRKAMATRIGSNRVN
> ILIRCTXXXXXXXXXXXXXXXXXXXXXXXXXNPYLGWWCYIFCIFR
>
> I don't like the Xs as they represent unspecified amino acids. Is there an input parameter to tell the program to report only the regions before and after the Xs ?
>
> In addition (and maybe this is beyond the scope of this mailing list) what is the biological meaning of such Xs ?

What was the input sequence like? Was there a stretch of NNNNN perhaps?

Peter



      



From pmr at ebi.ac.uk  Tue Jan 12 09:15:28 2010
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 12 Jan 2010 14:15:28 +0000
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the
 ORF sequence
In-Reply-To: <488158.80632.qm@web65501.mail.ac4.yahoo.com>
References: <480812.49255.qm@web65508.mail.ac4.yahoo.com>	<320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>
	<488158.80632.qm@web65501.mail.ac4.yahoo.com>
Message-ID: <4B4C8400.3080602@ebi.ac.uk>

Hi Avi,

> The input is a simple fasta file with only A,C,T,G letters and
> nothing else, so I wouldn't expect any Xs. In addition, even if there
> would be Ns (and there are no Ns) the program cannot know if such Ns
> do not include stopcodons so it should not consider them as part of an ORF.

>>> 00001_3 [803 - 1120]
>> LARLRFVVLGNSFIASAKGWSTPYGPTTFGPFRSCIYPRVFRSTRVRKAMATRIGSNRVN
>> ILIRCTXXXXXXXXXXXXXXXXXXXXXXXXXNPYLGWWCYIFCIFR

That suggests the Xs have all come from stop codons.

There are other possibilities, including a badly formatted input file
(perhaps two sequences and descriptions read as one).

We do need to see the input file to know where those Xs are from.

Peter Rice

From fungazid at yahoo.com  Wed Jan 13 11:30:26 2010
From: fungazid at yahoo.com (Fungazid)
Date: Wed, 13 Jan 2010 08:30:26 -0800 (PST)
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the
	ORF sequence
In-Reply-To: <4B4C8400.3080602@ebi.ac.uk>
References: <480812.49255.qm@web65508.mail.ac4.yahoo.com>
	<320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>
	<488158.80632.qm@web65501.mail.ac4.yahoo.com>
	<4B4C8400.3080602@ebi.ac.uk>
Message-ID: <3651.97395.qm@web65505.mail.ac4.yahoo.com>

Thanks Peter,

I made a mistake and took a repeat masked contigs instead of the original contigs, and they indeed had Ns. Sorry for the mess (still, I?am looking for an option where Ns are not be included in?the ORF).

Avi



----- Original Message ----
From: Peter Rice <pmr at ebi.ac.uk>
To: Fungazid <fungazid at yahoo.com>
Cc: emboss at lists.open-bio.org
Sent: Tue, January 12, 2010 4:15:28 PM
Subject: Re: [EMBOSS] getorf includes unspecified amino acids as part of the ORF sequence

Hi Avi,

> The input is a simple fasta file with only A,C,T,G letters and
> nothing else, so I wouldn't expect any Xs. In addition, even if there
> would be Ns (and there are no Ns) the program cannot know if such Ns
> do not include stopcodons so it should not consider them as part of an ORF.

>>> 00001_3 [803 - 1120]
>> LARLRFVVLGNSFIASAKGWSTPYGPTTFGPFRSCIYPRVFRSTRVRKAMATRIGSNRVN
>> ILIRCTXXXXXXXXXXXXXXXXXXXXXXXXXNPYLGWWCYIFCIFR

That suggests the Xs have all come from stop codons.

There are other possibilities, including a badly formatted input file
(perhaps two sequences and descriptions read as one).

We do need to see the input file to know where those Xs are from.

Peter Rice



      



From pmr at ebi.ac.uk  Wed Jan 13 12:36:08 2010
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 13 Jan 2010 17:36:08 +0000
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the
 ORF sequence
In-Reply-To: <3651.97395.qm@web65505.mail.ac4.yahoo.com>
References: <480812.49255.qm@web65508.mail.ac4.yahoo.com>
	<320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>
	<488158.80632.qm@web65501.mail.ac4.yahoo.com>
	<4B4C8400.3080602@ebi.ac.uk>
	<3651.97395.qm@web65505.mail.ac4.yahoo.com>
Message-ID: <4B4E0488.1070409@ebi.ac.uk>

Hi Avi,

> I made a mistake and took a repeat masked contigs instead of the
> original contigs, and they indeed had Ns. Sorry for the mess (still,
> I am looking for an option where Ns are not be included in the ORF).

Just too late for the next EMBOSS release (in preparation), but a good 
suggestion for July.

We should look at adding options to all the translation programs for 
repeat-masked inputs. This probably means treating each unmasked (non N) 
region as a separate sequence with options to include an OREF running up 
to the Ns or to stop at the last stop codon, and the same for the start 
of an ORF. Similar to handling the start and end of the whole sequence.

Hope that will help

Peter

From ajb at ebi.ac.uk  Fri Jan 15 06:59:26 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Fri, 15 Jan 2010 11:59:26 -0000 (UTC)
Subject: [EMBOSS] EMBOSS 6.2.0 released
Message-ID: <47510.86.26.12.63.1263556766.squirrel@webmail.ebi.ac.uk>

EMBOSS 6.2.0 is now available. You can download it from
our ftp server:

  ftp://emboss.open-bio.org:/pub/EMBOSS/

Its associated (optional) EMBASSY packages are in the same directory.

The native Microsoft windows port (mEMBOSS) can be downloaded from the
directory:

  ftp://emboss.open-bio.org:/pub/EMBOSS/windows/

6.2.0 is primarily a maintenance release but does contain many
new features listed in the attached changelog.

Alan
-------------- next part --------------
A non-text attachment was scrubbed...
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Type: application/octet-stream
Size: 9007 bytes
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URL: <http://lists.open-bio.org/pipermail/emboss/attachments/20100115/f4e668ce/attachment.obj>

From biopython at maubp.freeserve.co.uk  Fri Jan 15 07:34:32 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 15 Jan 2010 12:34:32 +0000
Subject: [EMBOSS] Many-to-many with needle and water
In-Reply-To: <4A51D360.1050107@ebi.ac.uk>
References: <320fb6e00907060312l5506c766i1c4a4ff48fba8c7e@mail.gmail.com>
	<4A51D360.1050107@ebi.ac.uk>
Message-ID: <320fb6e01001150434y2ecb268ai460fbf962895d6a6@mail.gmail.com>

On Mon, Jul 6, 2009 at 10:35 AM, Peter Rice <pmr at ebi.ac.uk> wrote:
>
> Peter Cock or biopython wrote:
>> Hi Peter R. et al,
>>
>> I gather EMBOSS is looking for feedback for new applications (given
>> the recent funding from the BBSRC - congratulations again). How about
>> suggestions for extensions to existing EMBOSS applications?
>>
>> I've used bits of EMBOSS for several years now (thank you!). Something
>> I have sometimes wanted to do is a many-to-many pairwise sequence
>> alignment with the EMBOSS tools needle and water.
>>
>> Right now, needle and water take two files (here referred to as A and
>> B), file A has just one sequence, and file B can have one or more
>> sequences. I'd like to be able to supply two files both with multiple
>> entries, and have needle/water do pairwise alignments between all the
>> sequences in A against all the sequences in B. This might be useful
>> for finding reciprocal best hits in comparative genomics (as an slower
>> but exact alternative to FASTA or BLAST).
>
> The application is easy to add (after the release)
>
> The usual problem with all-against-all is that it involves loading one
> of the inputs as a sequence set entirely in memory - to avoid reading
> one input many times over.
>
> We have an application supermatcher which does this - the first sequence
> is streamed through, the second is a sequence set loaded into memory. It
> uses work matching to find seed alignments then runs a limited alignment
> around the hits.
>
> superwater would be a possible name (or superneedle).

Is see EMBOSS 6.2 has a new tool "needleall" (although if there is a
matching "waterall" the changelog doesn't mention it):
http://lists.open-bio.org/pipermail/emboss/2010-January/003823.html

I'll have to try this out...

Peter

From ajb at ebi.ac.uk  Wed Jan 20 10:21:20 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 20 Jan 2010 15:21:20 -0000 (UTC)
Subject: [EMBOSS] mEMBOSS 6.2.0.1 available
Message-ID: <54507.86.26.12.63.1264000880.squirrel@webmail.ebi.ac.uk>

mEMBOSS 6.0.2.1 is available from:

ftp://emboss.open-bio.org/pub/EMBOSS/windows/

It fixes a library problem that  prevented emma from
launching clustal. There are also a few minor updates.

Alan



From fungazid at yahoo.com  Mon Jan 11 14:26:34 2010
From: fungazid at yahoo.com (Fungazid)
Date: Mon, 11 Jan 2010 06:26:34 -0800 (PST)
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the ORF
	sequence
Message-ID: <480812.49255.qm@web65508.mail.ac4.yahoo.com>

Hello people,

I just installed emboss on linux ubuntu (using the ubuntu synaptic package manager). I am using the getorf program, and I see it gives me this kind of output lines:

>00001_3 [803 - 1120] 
LARLRFVVLGNSFIASAKGWSTPYGPTTFGPFRSCIYPRVFRSTRVRKAMATRIGSNRVN
ILIRCTXXXXXXXXXXXXXXXXXXXXXXXXXNPYLGWWCYIFCIFR 

I don't like the Xs as they represent unspecified amino acids. Is there an input parameter to tell the program to report only the regions before and after the Xs ?

In addition (and maybe this is beyond the scope of this mailing list) what is the biological meaning of such Xs ?


thanks,
Avi




      



From biopython at maubp.freeserve.co.uk  Mon Jan 11 15:53:02 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 11 Jan 2010 15:53:02 +0000
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the
	ORF sequence
In-Reply-To: <480812.49255.qm@web65508.mail.ac4.yahoo.com>
References: <480812.49255.qm@web65508.mail.ac4.yahoo.com>
Message-ID: <320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>

On Mon, Jan 11, 2010 at 2:26 PM, Fungazid <fungazid at yahoo.com> wrote:
>
> Hello people,
>
> I just installed emboss on linux ubuntu (using the ubuntu synaptic package manager). I am using the getorf program, and I see it gives me this kind of output lines:
>
>>00001_3 [803 - 1120]
> LARLRFVVLGNSFIASAKGWSTPYGPTTFGPFRSCIYPRVFRSTRVRKAMATRIGSNRVN
> ILIRCTXXXXXXXXXXXXXXXXXXXXXXXXXNPYLGWWCYIFCIFR
>
> I don't like the Xs as they represent unspecified amino acids. Is there an input parameter to tell the program to report only the regions before and after the Xs ?
>
> In addition (and maybe this is beyond the scope of this mailing list) what is the biological meaning of such Xs ?

What was the input sequence like? Was there a stretch of NNNNN perhaps?

Peter


From fungazid at yahoo.com  Tue Jan 12 13:33:14 2010
From: fungazid at yahoo.com (Fungazid)
Date: Tue, 12 Jan 2010 05:33:14 -0800 (PST)
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the
	ORF sequence
In-Reply-To: <320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>
References: <480812.49255.qm@web65508.mail.ac4.yahoo.com>
	<320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>
Message-ID: <488158.80632.qm@web65501.mail.ac4.yahoo.com>

Hi Peter,

The input is a simple?fasta file with only A,C,T,G letters and nothing else, so I wouldn't expect any Xs. In addition, even if there?would be?Ns (and there are no Ns) the program cannot know if such Ns do not include stop codons so it should not consider them as part of an?ORF.

Best,
Avi



----- Original Message ----
From: Peter <biopython at maubp.freeserve.co.uk>
To: Fungazid <fungazid at yahoo.com>
Cc: emboss at lists.open-bio.org
Sent: Mon, January 11, 2010 5:53:02 PM
Subject: Re: [EMBOSS] getorf includes unspecified amino acids as part of the ORF sequence

On Mon, Jan 11, 2010 at 2:26 PM, Fungazid <fungazid at yahoo.com> wrote:
>
> Hello people,
>
> I just installed emboss on linux ubuntu (using the ubuntu synaptic package manager). I am using the getorf program, and I see it gives me this kind of output lines:
>
>>00001_3 [803 - 1120]
> LARLRFVVLGNSFIASAKGWSTPYGPTTFGPFRSCIYPRVFRSTRVRKAMATRIGSNRVN
> ILIRCTXXXXXXXXXXXXXXXXXXXXXXXXXNPYLGWWCYIFCIFR
>
> I don't like the Xs as they represent unspecified amino acids. Is there an input parameter to tell the program to report only the regions before and after the Xs ?
>
> In addition (and maybe this is beyond the scope of this mailing list) what is the biological meaning of such Xs ?

What was the input sequence like? Was there a stretch of NNNNN perhaps?

Peter



      




From pmr at ebi.ac.uk  Tue Jan 12 14:15:28 2010
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 12 Jan 2010 14:15:28 +0000
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the
 ORF sequence
In-Reply-To: <488158.80632.qm@web65501.mail.ac4.yahoo.com>
References: <480812.49255.qm@web65508.mail.ac4.yahoo.com>	<320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>
	<488158.80632.qm@web65501.mail.ac4.yahoo.com>
Message-ID: <4B4C8400.3080602@ebi.ac.uk>

Hi Avi,

> The input is a simple fasta file with only A,C,T,G letters and
> nothing else, so I wouldn't expect any Xs. In addition, even if there
> would be Ns (and there are no Ns) the program cannot know if such Ns
> do not include stopcodons so it should not consider them as part of an ORF.

>>> 00001_3 [803 - 1120]
>> LARLRFVVLGNSFIASAKGWSTPYGPTTFGPFRSCIYPRVFRSTRVRKAMATRIGSNRVN
>> ILIRCTXXXXXXXXXXXXXXXXXXXXXXXXXNPYLGWWCYIFCIFR

That suggests the Xs have all come from stop codons.

There are other possibilities, including a badly formatted input file
(perhaps two sequences and descriptions read as one).

We do need to see the input file to know where those Xs are from.

Peter Rice


From fungazid at yahoo.com  Wed Jan 13 16:30:26 2010
From: fungazid at yahoo.com (Fungazid)
Date: Wed, 13 Jan 2010 08:30:26 -0800 (PST)
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the
	ORF sequence
In-Reply-To: <4B4C8400.3080602@ebi.ac.uk>
References: <480812.49255.qm@web65508.mail.ac4.yahoo.com>
	<320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>
	<488158.80632.qm@web65501.mail.ac4.yahoo.com>
	<4B4C8400.3080602@ebi.ac.uk>
Message-ID: <3651.97395.qm@web65505.mail.ac4.yahoo.com>

Thanks Peter,

I made a mistake and took a repeat masked contigs instead of the original contigs, and they indeed had Ns. Sorry for the mess (still, I?am looking for an option where Ns are not be included in?the ORF).

Avi



----- Original Message ----
From: Peter Rice <pmr at ebi.ac.uk>
To: Fungazid <fungazid at yahoo.com>
Cc: emboss at lists.open-bio.org
Sent: Tue, January 12, 2010 4:15:28 PM
Subject: Re: [EMBOSS] getorf includes unspecified amino acids as part of the ORF sequence

Hi Avi,

> The input is a simple fasta file with only A,C,T,G letters and
> nothing else, so I wouldn't expect any Xs. In addition, even if there
> would be Ns (and there are no Ns) the program cannot know if such Ns
> do not include stopcodons so it should not consider them as part of an ORF.

>>> 00001_3 [803 - 1120]
>> LARLRFVVLGNSFIASAKGWSTPYGPTTFGPFRSCIYPRVFRSTRVRKAMATRIGSNRVN
>> ILIRCTXXXXXXXXXXXXXXXXXXXXXXXXXNPYLGWWCYIFCIFR

That suggests the Xs have all come from stop codons.

There are other possibilities, including a badly formatted input file
(perhaps two sequences and descriptions read as one).

We do need to see the input file to know where those Xs are from.

Peter Rice



      




From pmr at ebi.ac.uk  Wed Jan 13 17:36:08 2010
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 13 Jan 2010 17:36:08 +0000
Subject: [EMBOSS] getorf includes unspecified amino acids as part of the
 ORF sequence
In-Reply-To: <3651.97395.qm@web65505.mail.ac4.yahoo.com>
References: <480812.49255.qm@web65508.mail.ac4.yahoo.com>
	<320fb6e01001110753s6c2f9939i7e4a619896794007@mail.gmail.com>
	<488158.80632.qm@web65501.mail.ac4.yahoo.com>
	<4B4C8400.3080602@ebi.ac.uk>
	<3651.97395.qm@web65505.mail.ac4.yahoo.com>
Message-ID: <4B4E0488.1070409@ebi.ac.uk>

Hi Avi,

> I made a mistake and took a repeat masked contigs instead of the
> original contigs, and they indeed had Ns. Sorry for the mess (still,
> I am looking for an option where Ns are not be included in the ORF).

Just too late for the next EMBOSS release (in preparation), but a good 
suggestion for July.

We should look at adding options to all the translation programs for 
repeat-masked inputs. This probably means treating each unmasked (non N) 
region as a separate sequence with options to include an OREF running up 
to the Ns or to stop at the last stop codon, and the same for the start 
of an ORF. Similar to handling the start and end of the whole sequence.

Hope that will help

Peter


From ajb at ebi.ac.uk  Fri Jan 15 11:59:26 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Fri, 15 Jan 2010 11:59:26 -0000 (UTC)
Subject: [EMBOSS] EMBOSS 6.2.0 released
Message-ID: <47510.86.26.12.63.1263556766.squirrel@webmail.ebi.ac.uk>

EMBOSS 6.2.0 is now available. You can download it from
our ftp server:

  ftp://emboss.open-bio.org:/pub/EMBOSS/

Its associated (optional) EMBASSY packages are in the same directory.

The native Microsoft windows port (mEMBOSS) can be downloaded from the
directory:

  ftp://emboss.open-bio.org:/pub/EMBOSS/windows/

6.2.0 is primarily a maintenance release but does contain many
new features listed in the attached changelog.

Alan
-------------- next part --------------
A non-text attachment was scrubbed...
Name: changelog
Type: application/octet-stream
Size: 9007 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/emboss/attachments/20100115/f4e668ce/attachment-0002.obj>

From biopython at maubp.freeserve.co.uk  Fri Jan 15 12:34:32 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 15 Jan 2010 12:34:32 +0000
Subject: [EMBOSS] Many-to-many with needle and water
In-Reply-To: <4A51D360.1050107@ebi.ac.uk>
References: <320fb6e00907060312l5506c766i1c4a4ff48fba8c7e@mail.gmail.com>
	<4A51D360.1050107@ebi.ac.uk>
Message-ID: <320fb6e01001150434y2ecb268ai460fbf962895d6a6@mail.gmail.com>

On Mon, Jul 6, 2009 at 10:35 AM, Peter Rice <pmr at ebi.ac.uk> wrote:
>
> Peter Cock or biopython wrote:
>> Hi Peter R. et al,
>>
>> I gather EMBOSS is looking for feedback for new applications (given
>> the recent funding from the BBSRC - congratulations again). How about
>> suggestions for extensions to existing EMBOSS applications?
>>
>> I've used bits of EMBOSS for several years now (thank you!). Something
>> I have sometimes wanted to do is a many-to-many pairwise sequence
>> alignment with the EMBOSS tools needle and water.
>>
>> Right now, needle and water take two files (here referred to as A and
>> B), file A has just one sequence, and file B can have one or more
>> sequences. I'd like to be able to supply two files both with multiple
>> entries, and have needle/water do pairwise alignments between all the
>> sequences in A against all the sequences in B. This might be useful
>> for finding reciprocal best hits in comparative genomics (as an slower
>> but exact alternative to FASTA or BLAST).
>
> The application is easy to add (after the release)
>
> The usual problem with all-against-all is that it involves loading one
> of the inputs as a sequence set entirely in memory - to avoid reading
> one input many times over.
>
> We have an application supermatcher which does this - the first sequence
> is streamed through, the second is a sequence set loaded into memory. It
> uses work matching to find seed alignments then runs a limited alignment
> around the hits.
>
> superwater would be a possible name (or superneedle).

Is see EMBOSS 6.2 has a new tool "needleall" (although if there is a
matching "waterall" the changelog doesn't mention it):
http://lists.open-bio.org/pipermail/emboss/2010-January/003823.html

I'll have to try this out...

Peter


From ajb at ebi.ac.uk  Wed Jan 20 15:21:20 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 20 Jan 2010 15:21:20 -0000 (UTC)
Subject: [EMBOSS] mEMBOSS 6.2.0.1 available
Message-ID: <54507.86.26.12.63.1264000880.squirrel@webmail.ebi.ac.uk>

mEMBOSS 6.0.2.1 is available from:

ftp://emboss.open-bio.org/pub/EMBOSS/windows/

It fixes a library problem that  prevented emma from
launching clustal. There are also a few minor updates.

Alan