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From: rak@sun1.ruf.uni-freiburg.de (Bodo Rak)
Newsgroups: bionet.software
Subject: Re: bug in tfasta
Message-ID: <1991Jan25.154220.3629@sun1.ruf.uni-freiburg.de>
Date: 25 Jan 91 15:42:20 GMT
References: <1991Jan23.184909.1286@murdoch.acc.Virginia.EDU>
Organization: Rechenzentrum der Universitaet Freiburg, Deutschland
Lines: 29

wrp@biochsn.acc.Virginia.EDU (William R. Pearson) writes:


>A minor bug in tfasta has been discovered (that hid for about
>four years).  It causes the program to core-dump when it encounters
>a DNA sequence shorter than 5 nt.  (Apparently there are several
>very short sequences in recent releases from genbank.)

>The bug affects both the older fasta14 and the newer fasta15,
>and revised versions of both have been posted for anonymous ftp in
>uvaarpa.virginia.EDU:/public_access/fasta14d.shar(.Z) or fasta15b.shar(.Z).
>(The IP address of uvaarpa is 128.143.2.7)

>Bill Pearson

We run TFASTA (version 1.4a of February 1990) on a PC and found that the 
program crashes when it encounters entry ECG24 (AC: K01130) in the EMBL data 
base. The sequence length of this entry is 5 nt. We had to regularly delete 
this entry in new releases of the data base. I therefore asked Rainer Fuchs 
at EMBL a while ago whether it would be possible to remove this entry,
which is probably of no informational value to anyone.

(BTW: We also use Fasta - in batch runs - on a PC to search the whole data 
base and find it very convenient. The average run takes about 20 minutes 
so that quite a number of jobs can be done over night. We mainly use mail-fasta
to run our sequences against new entries.)

Bodo Rak