Question: Problem with SMART
0
gravatar for alejocn5
4.8 years ago by
alejocn50
Colombia
alejocn50 wrote:

Im trying to use SMART hmm profiles in a amino acid sequence, but when I use hmmsearch with thist profiles I can see this error:

Error: bad file format in HMM file

anyone knows how i can correct this error?

error hmmsearch hmm smart • 1.2k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by alejocn50

Did you hmmpress you HMM profile?

edit: in general, you should provide more details, such as command used, which HMM profile, and so forth.

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by h.mon32k
0
gravatar for alejocn5
4.8 years ago by
alejocn50
Colombia
alejocn50 wrote:

thanks for answer

Yes, i generate the binaries files with hmmerpress,

I use this command in hmmsearch

hmmsearch -o -domtblout out.hmmer /smart/6.2/smart.HMMs Data/secuence.tasta

these HMM profile of SMART are inte databases of interproscan or you can download this from the page www.embl-em.de

The hidden markov model look like (i am not sure if hmmsearch recognizes this format HMMER2.0, and this is the problem)

HMMER2.0

NAME 14_3_3

ACC SM00101

DESC 14-3-3 homologues

LENG 249

ALPH Amino

RF no

CS no COM /usr/people/jschultz/comp/domdb/hmmer-2.0/binaries/hmmbuild 1433_4.HMM /coot1/adm_bork/www/htdocs/SMART_DATA/alignments/1433_4.aln COM /usr/people/jschultz/comp/domdb/hmmer-2.0/binaries/hmmcalibrate 1433_4.HMM NSEQ 6

DATE Mon Oct 12 18:40:49 1998

XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4

NULT -4 -8455

NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 EVD -194.837555 0.136408 HMM A C D E F G H I K L M N P Q R S T V W Y

thaks

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by alejocn50
0
gravatar for alejocn5
4.8 years ago by
alejocn50
Colombia
alejocn50 wrote:

HMMER2.0

NAME 14_3_3

ACC SM00101

DESC 14-3-3 homologues

LENG 249

ALPH Amino

RF no

CS no

ADD COMMENTlink written 4.8 years ago by alejocn50
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