Fasta2Ace? and Using Blixem in AceDB

Steven A. Mauget smauget at lbk.ars.usda.gov
Mon Jan 20 03:50:21 EST 2003


Dear AceDB Users:

I don't have a background in biology, but am setting up a bioinformatics
analysis chain (phred - lucy - TIGR_Assembler - WU-Blast) for a group of
plant geneticists at our lab. I'm trying to enter the results of blastn
searchs into acedb, and I'd like to access blixem within acedb to
evaluate and visualize the results.

So far, I've been able to convert blastn output into .ace files using
MSPcrunch -4 and have loaded the resulting  files into acedb. Problem
is, I also understand that blixem  requires our query sequence input
data that blastn was matching NCBI sequence data against. These
sequences are contained in a fasta file that was one of the outputs of
TIGR_Assembler. So, I'm guessing that my next step is to parse that
fasta file into an ace file. Looking over the acedb.org web site's page
regarding loading .ace files doesn't say anything about fasta parsing
that I can see. In looking over the bionet usegroup I seem to remember a
reply that basically said these parsers have to be written by the user
on an as-needed basis. After browsing thru Mary  O' Callaghan's 'Guide
to Models and Ace Files' it seems that writing such a parser wouldn't be
too hard. Two Questions:

I) Am I on the right track in trying to make blixem work within acedb? I
know people have had problems similar to mine before (e.g. Florent
Crepineau queried this usegroup with a similar question a few years
back, but I can't find a reply that described how his problem was
resolved).

II) Does anyone out there know of a 'fasta2ace' parser that has already
been written?


Thanks in advance for any help or advice,


Steve Mauget

--
########### smauget at lbk.ars.usda.gov ##############
Steve Mauget
USDA - Agricultural Research Service
3810 4th Street
Lubbock, Texas, 79415
1-806-723-5237
########### smauget at lbk.ars.usda.gov ##############


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