[BiO BB] RE: BiO_Bulletin_Board digest, Vol 1 #584 - 4 msgs

Venkata Satagopam venkata.satagopam at lionbioscience.com
Mon Dec 15 05:19:34 EST 2003


Hello Jordan,
Yes, it is possible, but first you have to create a Fasta file
out of these Genbank files gbpln[1-9].seq. So that means you
have to extract all the sequences from above files and store
them in a FASTA format. Once you have fasta file, then you have
to create blastble by using formatdb by using following command

formatdb -i <fastafile_name> -p F 

then you are able to blast against this fastafile. I hope this
will help you, if you need more info please contact me either
in the group or @ satagopam_p at yahoo.com

regards
venkata 
 

-----Original Message-----
From: bio_bulletin_board-admin at bioinformatics.org
[mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of
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Sent: Friday, December 12, 2003 6:01 PM
To: bio_bulletin_board at bioinformatics.org
Subject: BiO_Bulletin_Board digest, Vol 1 #584 - 4 msgs


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Today's Topics:

   1. Is it possible to Blast against genBank files (jordan swanson)
   2. Re: Is it possible to Blast against genBank files (Iddo Friedberg)
   3. xylitol enzyme (=?iso-8859-1?q?John=20Kecops=20Kleinsteuber?=)
   4. remove (Derek Pyper)

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Message: 1
Date: Thu, 11 Dec 2003 15:44:15 -0800 (PST)
From: jordan swanson <jordanmswanson at yahoo.com>
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] Is it possible to Blast against genBank files
Reply-To: bio_bulletin_board at bioinformatics.org

I've downloaded and installed blast and some FASTA
databases for a lab I'm working for.  I have a user
who is blasting (using blastx) against a list of
clones.  Unfortunately, the database files I
downloaded do not contain enough information for
her(because they are fasta format)

This leads me to believe that I need a local copy of
the genBank files.  I've downloaded gbpln[1-9].seq
from NCBI. (we only need plant files).  Is it possible
to blast against these gb files?  Also, what options
do I need to use on formatdb to create the correct
index files?

If my questions are out of place here, let me know and
I'll desist.

-Jordan M Swanson

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Message: 2
Date: Thu, 11 Dec 2003 15:57:46 -0800
From: Iddo Friedberg <idoerg at burnham.org>
To: bio_bulletin_board at bioinformatics.org
Subject: Re: [BiO BB] Is it possible to Blast against genBank files
Reply-To: bio_bulletin_board at bioinformatics.org



jordan swanson wrote:
> I've downloaded and installed blast and some FASTA
> databases for a lab I'm working for.  I have a user
> who is blasting (using blastx) against a list of
> clones.  Unfortunately, the database files I
> downloaded do not contain enough information for
> her(because they are fasta format)

You mean that the BLAST results only have the Fasta file annotation in
them. Well, AFAIK, the only input to formatdb is Fasta or ASN.1. The
output, anyhow, would be a one-liner.

How about giving her the output in HTML (-T option)? blast automatically
builds a link from each hit to the NCBI page. So using a browser, your
coworker can skim the one-line annotation, and then click & delve into
the more interesting ones.


>
> This leads me to believe that I need a local copy of
> the genBank files.  I've downloaded gbpln[1-9].seq
> from NCBI. (we only need plant files).  Is it possible
> to blast against these gb files?  Also, what options
> do I need to use on formatdb to create the correct
> index files?
>

You can only formatdb from ASN.1 or Fasta formats.


> If my questions are out of place here, let me know and
> I'll desist.
>
> -Jordan M Swanson
>
> __________________________________
> Do you Yahoo!?
> New Yahoo! Photos - easier uploading and sharing.
> http://photos.yahoo.com/
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>

--
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://ffas.ljcrf.edu/~iddo


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Message: 3
Date: Fri, 12 Dec 2003 02:45:56 +0000 (GMT)
From: =?iso-8859-1?q?John=20Kecops=20Kleinsteuber?= <johnkecops at yahoo.co.uk>
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] xylitol enzyme
Reply-To: bio_bulletin_board at bioinformatics.org

--0-814827070-1071197156=:24403
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

 Hi, I'm a student of Chemistry in University of Indonesia. Currently, I'm working my research about xylitol enzyme. I want to study its hidrolisis yield on rice beech. The problem is: I have trouble on many aspects. I don't know how to prepare the sample, and I don't know how to caracterize it result with HPLC. Is any one can help me? Please sent me your e-mail to me if you can help me with this xylitol enzyme. Thank you.


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--0-814827070-1071197156=:24403
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<DIV><STRONG>&nbsp;Hi, I'm a student of Chemistry in University of Indonesia. Currently, I'm working my research about xylitol enzyme. I want to study its hidrolisis yield on rice beech. The problem is: I have trouble on many aspects. I don't know how to prepare the sample, and I don't know how to caracterize it result with HPLC. Is any one can help me? Please sent me your e-mail to me if you can help me with this xylitol enzyme. Thank you.</STRONG></DIV><p><hr size=1><font face="Arial" size="2">  <a href="http://uk.rd.yahoo.com/evt=21064/*http://btyahoo.yahoo.co.uk "><b> BT Yahoo! Broadband</b></a> - Save £80 when you order online today. Hurry! Offer ends 21st December 2003. The way the internet was meant to be.
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Message: 4
Date: Fri, 12 Dec 2003 07:41:53 -0800
From: Derek Pyper <derek at biotechrecruiter.org>
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] remove
Reply-To: bio_bulletin_board at bioinformatics.org

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Derek Pyper
Biotech Recruiters International, Inc.
Principal
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Fax          916-652-2178
Email:      Derek at biotech-recruiters.com
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-----Original Message-----
From: bio_bulletin_board-admin at bioinformatics.org
[mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of
Radhika Tallamraju
Sent: Friday, December 05, 2003 8:34 AM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] help regarding MEME program

Can anyone suggest me how to construct log odds matrix for a given
consensus sequence. I need this to run MAST program.

Regards,
Radhika.


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End of BiO_Bulletin_Board Digest

---
Venkata Pardhasaradhi Satagopam, 
Bioinformatics Scientist, 
Genomics IT Research, 
Office Address :LION Bioscience AG, Waldhofer Str.98,69123 Heidelberg,GERMANY. Tel: 0049-(0)6221 4038 414
Home Address :Fritz-Frey-Str.8/112.301.01, 69121 Heidelberg, GERMANY. Tel:0049-(0)6221 729667
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