[BiO BB] Articles invited for a Bioinformatics book
Mathura, Venkatarajan S.
vsmathur at UTMB.EDU
Fri Jun 3 10:30:08 EDT 2005
Articles are invited for a book titled "Introduction to Bioinformatics: A workbook approach"
to be published by Springer. The book is expected to be published by the end of this year.
If you have an interesting Bioinformatics application, please include a short manuscript (1-2 pages)
using the format enclosed. For details and your intent to write please contact: Venkat Mathura (venkat at rfdn.org)
Details and Format:
Book title
Introduction to Bioinformatics: A workbook approach
Targeted audience
Undergraduate and graduate students
Publisher
Springer
Date to be published
End of 2005
Corresponding Editor
Venkat Mathura
Roskamp Institute
Sarasota, FL 34243
USA
Email: venkat at rfdn.org
Phone: 9417522949
How to contribute
1-2 pages about an Application/Tool/Software package in Bioinformatics can be submitted in the following format:
Author and Affiliation:
eg. John Doe
Center for Biocomputing
University of Texas Austin
Austin, Texas
Application/Tool/Package name:
ClustalNew (v 1.0)
Short Introduction & Algorithm:
Include algorithms used in the tool or proved citation of paper published.
Detail features available in the tool
References should be (author, year) style. If there are more than two authors use et al.
Availability (web site):
http://newsite.bioinfo.org/ClustalNew.html
Application in Bioinformatics
To perform multiple alignment of protein or DNA sequences…….
Usage (give a biological application or an example)
We will describe here how to create multiple alignment of SH3 domain protein…..
Exercise (include one or more question to which the student should address)
Perform a multiple aligment of the following sequence (genbank_id1, genbank_id2) and identify conserved segments……….
Figure legends and tables
Figure 1. Screen capture of multiple alignment……….
References
Doe J. “ClustalNew: A fast multiple sequence alignment tool” J computational Biology 2005 33:192-193
Note
1. Please check with the editors regarding suitability of your application.
2. The editors reserve rights to add, delete, reformat or exclude contents.
3. Articles that do not meet scientific standards will be rejected.
4. You may write about applications developed by others (to reduce redundancy please check with the editor)
5. Reference style should be consistent.
6. Figures and tables should be numbered appropriately.
7. Please submit your manuscript as word document (double spaced) by email to venkat at rfdn.org.
8. The authors will be notified about the acceptance and inclusion in the book as soon as possible.
9. For questions please contact: venkat at rfdn.org
-----Original Message-----
From: bio_bulletin_board-bounces+vsmathur=utmb.edu at bioinformatics.org on behalf of bio_bulletin_board-request at bioinformatics.org
Sent: Thu 6/2/2005 11:07 AM
To: bio_bulletin_board at bioinformatics.org
Cc:
Subject: BiO_Bulletin_Board Digest, Vol 8, Issue 1
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Today's Topics:
1. Parsing NCBI-BLAST -m 3 or -m 4 option (Eray Tuzun)
2. Re: Parsing NCBI-BLAST -m 3 or -m 4 option (Iddo Friedberg)
----------------------------------------------------------------------
Message: 1
Date: Wed, 1 Jun 2005 21:40:27 -0400 (EDT)
From: Eray Tuzun <ext29 at eecs.cwru.edu>
Subject: [BiO BB] Parsing NCBI-BLAST -m 3 or -m 4 option
To: "The general forum at Bioinformatics.Org"
<bio_bulletin_board at bioinformatics.org>
Message-ID: <Pine.SOL.4.53.0506012138120.28868 at mozart>
Content-Type: text/plain; charset=us-ascii
I'd like to parse NCBI-Blast -m 3 option or -m 4 option. Is there any open
source programs for this?(C,Java or Perl)
Thanks,
Eray
ERAY TUZUN, MS
Senior Computer Specialist
Department of Genome Sciences
University of Washington
------------------------------
Message: 2
Date: Wed, 1 Jun 2005 20:46:16 -0700
From: Iddo Friedberg <idoerg at burnham.org>
Subject: Re: [BiO BB] Parsing NCBI-BLAST -m 3 or -m 4 option
To: "The general forum at Bioinformatics.Org"
<bio_bulletin_board at bioinformatics.org>
Cc: ext29 at eecs.cwru.edu
Message-ID:
<Pine.SGI.4.10.10506012043420.3298831-100000 at pines2.ljcrf.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Eray,
Check out bioperl.org / biojava.org for BLAST parsers.
Biopython has good BLAST parsers, but Python was not on your language
list.
HTH,
Iddo
--
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037, USA
Tel: Ư (858) 646 3100 x3516
Fax: Ư (858) 646 3171
http://ffas.ljcrf.edu/~iddo
-------------------------------------
Automated Protein Function Prediction Meeting, June 24, 2005
http://ffas.burnham.org/AFP
On Wed, 1 Jun 2005, Eray Tuzun wrote:
>
>
> I'd like to parse NCBI-Blast -m 3 option or -m 4 option. Is there any open
> source programs for this?(C,Java or Perl)
>
> Thanks,
> Eray
>
>
> ERAY TUZUN, MS
> Senior Computer Specialist
> Department of Genome Sciences
> University of Washington
> _______________________________________________
> Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
------------------------------
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End of BiO_Bulletin_Board Digest, Vol 8, Issue 1
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