[Bioperl-l] Clustalw && large sequence number

[nkuipers]

I mean no offense whatsoever, but I have to ask what use or significance you 
are aiming for with a 4000 sequence alignment.  Especially if they are fairly 
disparate, an alignment of that magnitude is not going to tell you much that's 
meaningful, in my opinion...again, this is sort of like playing devil's 
advocate, i am merely curious.

Regards,

Nathanael Kuipers
---
Center for Biomedical Research,
Dept. of Biology, University of Victoria,
Victoria BC Canada


>===== Original Message From Sally Li <sallyli97@yahoo.com> =====
>Hi, there,
>
>I received some messages related to this issue. Let me
>explain this problem in a more detail.
>
>Hardware: IBM eServer
>          Memory: 6 G
>          processors: 4 X 700 MH
>Software:
>
>    bioperl
>    clustalw 1.82
>
>Problem:
>  If the sequences number is large, like 4000
>sequences the program was running . But after a long
>run, it is hanging there for ever. No error messages
>appear.
>
>Notes: clustalw is ok to process less than 1000
>sequences. I have aligned 500 sequences ( Mouse
>genome) and it works fine. The performance and results
>are good to me. If some one can solve this problem, I
>believe it will help me and other people who are
>intersed in aligment for the huge sequence file.
>
>Thank you very much for your help.
>
>Sally
>
>
>--- Christopher J Moressi
><cmoressi@engineering.uiowa.edu> wrote:
>> Mrs Li.
>>
>> That is a large amount of sequences all right. I was
>> wondering if you could
>> give me the version of Clustalw you are using. I
>> know one of the older
>> version had some memory problems which in some
>> operation systems would cause
>> a core dump. Also, what are the error/debug
>> information are you receiving
>> from the program?
>>
>> If you feel ambitious, you might try using gdb to
>> check were the problem may
>> be. It wont take much time to figure out what piece
>> of code is causing the
>> problem, however, figuring out what it is doing and
>> why will take some
>> time..
>>
>> 	-Chris
>>
>>
>> -----Original Message-----
>> From: bioperl-l-admin@bioperl.org
>> [mailto:bioperl-l-admin@bioperl.org]On
>> Behalf Of Sally Li
>> Sent: Thursday, January 16, 2003 2:54 PM
>> To: bioperl-l@bioperl.org
>> Subject: [Bioperl-l] Clustalw && large sequence
>> number
>>
>>
>> Hi,
>>
>>  I have clustalw run in my Red Hat 8.0 of IBM
>> eServer
>>  which has 6 G memory. But I failed to get the
>> aligment
>> done if sequence number is big, like, 4000
>> sequences.
>>  Any  idea?
>>
>>  Thank you very much.
>>
>>  Sally
>>
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>
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