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Sendu Bala | 1 Jun 2007 10:06
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Re: ClustalW Score?

Kevin Brown wrote:
>> you're right --- it is not really my code, I was just 
>> elaborating Kevin's example --- it would probably need to be 
>> more specific or perhaps the last Score seen is sufficient 
>> for what one is trying to capture?
> 
> I took that code from a pairwise clustal alignment script that I wrote
> to deal with aligning a bunch of short sequences against a long one to
> see where they line up at.  When all of them were fed to Clustal the
> short sequences all ended up aligned to each other and not well aligned
> to the longer sequence.  I only saw one score in the output from the
> pairwise, so that is what I used to find a reasonable value.

Ok, well I've hedged my bets and used both. Now commited to CVS.
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Jean-Yves Sireau | 2 Jun 2007 04:39
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Genseq

Dear List members,

I would like to let you know of the formation of Genseq Ltd., a
bioinformatics company that will (in time!) offer genome sequencing to
high net worth individuals and bioinformatic analysis of the sequence
data to detect predisposition to illness.  The company's website is
www.genseq.co.uk

Genseq would be willing to sponsor bioperl, whether financially or by
providing resources, notably for any bioperl-related activities in the
Asia Pacific region.  Genseq's bioinformatics team will be based in
Cyberjaya (Malaysia), and we are in particular interested to promote
bioperl in Malaysia.  We are also actively recruiting at the moment
in Malaysia and India.

If there was sufficient demand, we would be willing to organise a
bioperl conference in Cyberjaya at the Cyberview Lodge
(www.cyberview-lodge.com), which would be the ideal place for such a
conference in Malaysia.

Looking forward to your comments, suggestions and proposals.

Best regards
Jean-Yves Sireau

--

-- 

Jean-Yves Sireau
CEO, Genseq Ltd.
www.genseq.co.uk
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Chris Fields | 2 Jun 2007 07:16
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EUtilities overhaul started

To anyone using Bio::DB::EUilities,

I am in the midst of a major overhaul to the various EUtilities tools  
and to Bio::DB::GenericWebDBI (the latter which I am forming into  
more or less a test bed for other database interfaces).  I'm about  
80% done at this point, and will likely start committing changes this  
coming week.

The overall interface will change (something I had warned about in  
the Bio::DB::EUtilities POD) but I am hoping it will be more  
intuitive and easier to use in the long run.  I'll describe the  
overall redesign and use in an upcoming HOWTO (as recommended by  
Brian a while back).

If anyone has any suggestions/ideas/flames, please let me know!

Cheers!

chris
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Chris Fields | 2 Jun 2007 16:39
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Re: EUtilities overhaul started

Yes, there are a few odd issues, though that's one I've not heard of  
yet.  You might try one of the sub-nucleotide databases (nuccore,  
nucest, nucgss).

I'll try looking into it and (if necessary) pester NCBI about it.   
I'll pass this on to the mail list to see if anyone else knows about  
the problem.

chris

On Jun 2, 2007, at 8:28 AM, Bernd Brandt wrote:

> Hi Chris,
>
> Thanks for your work on EUtilities.
> For a production task, I used EUtilitities directly (given your
> announced overhaul). I noticed a recent problem at NCBI (reported two
> weeks ago to NCBI, no reply yet). Possibly you may run into this with
> testing: if you ePOST gi ids to the EU server and then use this set in
> Esearch (using the query key) no results are returned for the
> nucleotide database.
> ESearches like "db=$db%23$QueryKey" typically fail if the $db is
> nucleotide (but work f $db='protein'). The XML output has Count 0 and
> an empty QueryTranslationSet for db=nucleotide only.
> For completeness, I attach a simple test script I used.
>
>
> Best regards,
> Bernd
>
(Continue reading)

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Chris Fields | 3 Jun 2007 06:51
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Re: EUtilities overhaul started

I can confirm this; however it only relates to the use of history  
with esearch and nucleotide (use of the history with other eutils  
seems to work fine); retrieving sequences via efetch is not  
affected.  If I find out anything more I'll post something on the  
mail list.

chris

On Jun 2, 2007, at 11:48 AM, Bernd Brandt wrote:

> I can confirm that using the correct sub-nucleotide database works
> (nuccore in my case).
> This seems to be a quite recent change/bug at NCBI. Until recently,
> db=nucleotide worked. Moreover, EInfo still lists nucleotide as valid
> db.
> It is not optimal to have to choose the sub-database and the searches
> work via the Entrez web-interface. Note that this problem is related
> to the ESearch and db=nucleotide.
>
> bernd
>
> On 6/2/07, Chris Fields <cjfields <at> uiuc.edu> wrote:
>> Yes, there are a few odd issues, though that's one I've not heard of
>> yet.  You might try one of the sub-nucleotide databases (nuccore,
>> nucest, nucgss).
>>
>> I'll try looking into it and (if necessary) pester NCBI about it.
>> I'll pass this on to the mail list to see if anyone else knows about
>> the problem.
>>
(Continue reading)

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Siddhartha Basu | 3 Jun 2007 16:44

Re: EUtilities overhaul started

On Sat, 2 Jun 2007 00:16:05 -0500
  Chris Fields <cjfields <at> uiuc.edu> wrote:
> To anyone using Bio::DB::EUilities,
> 
> I am in the midst of a major overhaul to the various 
>EUtilities tools  
> and to Bio::DB::GenericWebDBI (the latter which I am 
>forming into  
> more or less a test bed for other database interfaces). 
> I'm about  
> 80% done at this point, and will likely start committing 
>changes this  
> coming week.
> 
> The overall interface will change (something I had 
>warned about in  
> the Bio::DB::EUtilities POD) but I am hoping it will be 
>more  
> intuitive and easier to use in the long run.  I'll 
>describe the  
> overall redesign and use in an upcoming HOWTO (as 
>recommended by  
> Brian a while back).

Hi chris,
Being a frequent user of EUtilities, hopefully this api 
facelift and upcoming howto will definitely be more 
helpful.
Anyway, one thing i noticed that for each eutil call such 
as efetch,epost,esearch,esummary a new
(Continue reading)

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Chris Fields | 4 Jun 2007 01:52
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Re: EUtilities overhaul started

On Jun 3, 2007, at 9:44 AM, Siddhartha Basu wrote:

> ...
> Hi chris,
> Being a frequent user of EUtilities, hopefully this api facelift  
> and upcoming howto will definitely be more helpful.
> Anyway, one thing i noticed that for each eutil call such as  
> efetch,epost,esearch,esummary a new 'Bio::DB::Utilities' object has  
> to be
> instantiated. And thereafter it cannot be set during runtime such as
> $eutils->id('ids'), for example....
>
> my $eutils = Bio::DB::Eutilities->new ( -id => $id,
>                                        -eutil => 'esummary',
>                                        -db => 'protein',
>                                      );
> my $ct = $eutils->get_response->content();
>
> ## -- now i cannot do this...
> $eutils->id($newid);
> my $ct = $eutils->get_response->content();

I'll have to check up on that, though changing id() should work with  
the old API.  It won't matter with the new API (it works fine), but  
it is still troubling...

> Is the new api going to address something along this line or is  
> there currently anyway to reuse
> the object.
> Thanks again for this nice toolkit.
(Continue reading)

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Steve Chervitz | 4 Jun 2007 19:56
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Re: question about Bio::Restriction::Analysis

Hi Apurva,

I'm cc:ing the list to let others know you have found performance
issues with Bio::Restriction::Analysis. Ideally, we should focus on
addressing those issues rather than fixing a module that is now
deprecated.

But taking a quick look at my Bio::Tools::RestrictionEnzyme module,
I'm not sure why HpaII would give slower performance relative to other
non-ambiguous cutters. This enzyme has a 4-base recognition sequence
CCGG, and if you're feeding it a large CG-rich input sequence, that
could be a factor. To test, you might try using some other 4-base
cutters that aren't CG-rich (TaqI, TasI) or try some other input
sequences. There is no special flag to indicate that the enzyme is
non-ambiguous. The module handles that automatically.

Good luck,
Steve

On 6/4/07, Apurva Narechania <apurva <at> cshl.edu> wrote:
> Hi Rob and Steve,
>
> I was hoping you could answer a quick performance question regarding
> the Bio::Restriction::Analysis module. I have found that though this
> module works well, it is considerably slower than the deprecated
> Bio::Tools::RestrictionEnzyme. I see that there are two algorithms
> available to your module, and since I am using HpaII, a non-ambiguous
> enzyme, I thought I might find similar performance to the older,
> deprecated module, but I do not. Is it possible that I am not setting
> the non-ambiguous flag correctly? Does it need to be set in the first
(Continue reading)

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Tieu, Anh-Thu | 5 Jun 2007 10:14
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problems with image maps and IE 6 or higher

Hi, 

 I have a problem using the bioperl image maps function with the IE6 or and
 higher browser. It might be a more general problem with IE6 rather than with bioperl,
 but as I used bioperl to create my image maps, I thought I could still post this problem 
 here and ask for people's opinion. I wondered if anyone else faced the same problem and if
 possible if anyone could share their experiences and their solutions. 

  
<div>
<p><img src="/ggtc/tmp_bilder/19727dab708e1cbf567dd48480febb96.png" usemap="mapnameD064C01"
style="border:2px solid #CCCCCC;"/></p>
<map name="mapnameD064C01" id="mapnameD064C01">
<area shape="rect" coords="108,0,608,20" href="javascript:void(0)"
onclick="javascript:void(zmenu( 'scale' ));;return false;" title="scale " alt="scale " target="_blank"/>
<area shape="rect" coords="234,44,244,55" href="javascript:void(0)"
onclick="javascript:void(zmenu( 'alignment 5splk', '', 'seq_id: ', '', 'start: ', '', 'stop: 0', '',
'length:  bp', '', 'identity: ', '', 'e-v
alue: ' ));;return false;" title="alignment5 " alt="alignment5 " target="_blank"/>
<area shape="rect" coords="241,57,247,68" href="javascript:void(0)"
onclick="javascript:void(zmenu( 'alignment 5splk', '', 'seq_id: ', '', 'start: ', '', 'stop: 0', '',
'length:  bp', '', 'identity: ', '', 'e-v
alue: ' ));;return false;" title="integration_pt " alt="integration_pt " target="_blank"/>
<area shape="rect" coords="108,70,608,81" href="javascript:void(0)"
onclick="javascript:void(zmenu( 'Nphs1                                   ', '', 'ensembl_id: ENSMUSG00000006649', '', 'start:
30168485', '', '
stop: 30195968', '', 'length: 27483 bp' ));;return false;" title="gene " alt="gene " target="_blank"/>
<area shape="rect" coords="108,83,117,94" href="javascript:void(0)"
onclick="javascript:void(zmenu( 'exon1', '', 'start: 30168485', '', 'stop: 30169003', '', 'length:
518 bp' ));;return false;" title="exon1 " a
(Continue reading)

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Lincoln Stein | 5 Jun 2007 15:56
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Re: problems with image maps and IE 6 or higher

Hi Anh-Thu,

Could you send me a snippet of the code that is generating this imagemap? It
looks like you are relying on a javascript library for the zmenu() call, and
it may be that this library is in need of updating.

You might also consider replacing the library with Sheldon McKay's popup
balloon library, located at
http://www.wormbase.org/wiki/index.php/Balloon_Tooltips

Lincoln

On 6/5/07, Tieu, Anh-Thu <anhthu.tieu <at> gsf.de> wrote:
>
> Hi,
>
> I have a problem using the bioperl image maps function with the IE6 or and
> higher browser. It might be a more general problem with IE6 rather than
> with bioperl,
> but as I used bioperl to create my image maps, I thought I could still
> post this problem
> here and ask for people's opinion. I wondered if anyone else faced the
> same problem and if
> possible if anyone could share their experiences and their solutions.
>
>
> <div>
> <p><img src="/ggtc/tmp_bilder/19727dab708e1cbf567dd48480febb96.png"
> usemap="mapnameD064C01" style="border:2px solid #CCCCCC;"/></p>
> <map name="mapnameD064C01" id="mapnameD064C01">
(Continue reading)

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