Question: Where can I download HMM profile for different species?
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gravatar for allyson1115ar
4.4 years ago by
allyson1115ar20 wrote:

I would like to ask is there any database allow me to download HMM for different species such as: 1. Pan troglodytes 2. Pongo abelii 3. Rhinopithecus rexellana

genome hmm sequence profile species • 1.7k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by allyson1115ar20
1

It seems you can download this from HMMER. If so, get more information from their paper HMMER web server: 2015 update.

ADD REPLYlink written 4.4 years ago by Denise CS5.1k

I can't find any hmm link to download the above 3 species :/

ADD REPLYlink written 4.4 years ago by allyson1115ar20
1

Which kind of HMM profile are you looking for ? => I mean is it for coding genes ? For what purpose do you need it ? More precisely, which tool do you plan to use with ?

ADD REPLYlink written 4.4 years ago by Juke344.9k

i would like to include the hmm in snap ab initio gene predictor since the package doesn't provide the other species

ADD REPLYlink written 4.4 years ago by allyson1115ar20
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Each ab-initio tool has its own hmm profile format. And they don't necessarily use the same kind of information. So, I doubt you can use the profile coming from another tool as HMMER as suggested. I guess you are trying to annotate the gene coding. So the simplest is to create the profile yourself. Download the gff and the genome of your species (on Ensembl as example). Put the fasta sequence within the gff file as it should be (Introduced by the ##FASTA line at the end of the file). Then prepare the needed files to train snap by using the maker2zff.pl tool that is coming with the MAKER genome annotation tool package. You will get two output files:genome.ann and genome.dna Then to create the profile you will have to launch those commands:

fathom -categorize 1000 genome.ann genome.dna
    fathom -export 1000 -plus uni.ann uni.dna
    forge export.ann export.dna
    hmm-assembler.pl SPECIES . > SPECIES.hmm
ADD REPLYlink written 4.4 years ago by Juke344.9k

It sounds like a reasonable approach!

ADD REPLYlink written 4.4 years ago by dago2.6k

Which HMM do you need?

ADD REPLYlink written 4.4 years ago by dago2.6k

the 3 species in my question

ADD REPLYlink written 4.4 years ago by allyson1115ar20

Yes I understand, but do you need the HMM for the nucleotides seqs of all genes, for the proteins? Also, I am not sure you have hmm specific for these species, maybe you can try to use Pfam domains and start with that for gene annotation.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by dago2.6k
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