Question: How to search Pfam DB using list of accessions
0
gravatar for Medhat
3.7 years ago by
Medhat8.0k
Poland
Medhat8.0k wrote:

I have a list of accession numbers, how can I search for there function in Pfam db http://pfam.xfam.org/ as a bulk ?

for example:

If I have this accession PF07714.12 and I searched manually I will get;

A tyrosine kinase is an enzyme that can transfer a phosphate group from ATP to a protein in a cell. It functions as an "on" or "off" switch in many cellular functions. Tyrosine kinases are a subclass of protein kinase.

The phosphate group is attached to the amino acid tyrosine on the protein. Tyrosine kinases are a subgroup of the larger class of protein kinases that attach phosphate groups to other amino acids (serine and threonine). Phosphorylation of proteins by kinases is an important mechanism in communicating signals within a cell (signal transduction) and regulating cellular activity, such as cell division.

Protein kinases can become mutated, stuck in the "on" position, and cause unregulated growth of the cell, which is a necessary step for the development of cancer. Therefore, kinase inhibitors, such asimatinib, are often effective cancer treatments.

how can I do it for a list of accessions?

sequence gene • 2.4k views
ADD COMMENTlink modified 3.7 years ago by venu5.7k • written 3.7 years ago by Medhat8.0k
2
gravatar for venu
3.7 years ago by
venu5.7k
Germany
venu5.7k wrote:

Unlike what you have shown here, if one sentence description is enough to describe about the family you can use hmmfetch which first extract profiles and from that file you can separate ACC & DESC lines easily, ACC - accession id, DESC - description about family. Here ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release you can download all pfam family HMM profiles in one file, then use it as a source to extract families of your interest.

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by venu5.7k

do you mean something like this ;

 lcl|GRMZM2G155384_P02    486    517    486    520 PF01851.17  PC_rep            Repeat     1    32    35     21.5   0.00018   1 CL0020

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Medhat8.0k

Nope. Like following

    ACC   PF00406.17  DESC  Adenylate kinase

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by venu5.7k

the command should be ;

hmmfetch [options] <hmmfile> <key> (retrieves HMM named <key>)
hmmfetch -f [options] <hmmfile> <keyfile> (retrieves all HMMs listed in <keyfile>)

I think i shall use the second command but I used the first as a test

./hmmfetch ~/Downloads/pfam-files/Pfam-A.hmm PF07714.12

and the result was 

HMMER3/f [3.1b1 | May 2013]
NAME  PC_rep
ACC   PF01851.17
DESC  Proteasome/cyclosome repeat
LENG  35
ALPH  amino
RF    no
MM    no
CONS  yes
CS    yes
MAP   yes
DATE  Thu Oct 11 22:09:41 2012
NSEQ  157
EFFN  157.000000
CKSUM 3600983919
GA    20.70 20.70
TC    20.70 20.70
NC    20.60 20.60
STATS LOCAL MSV       -7.3958  0.73121
STATS LOCAL VITERBI   -7.8668  0.73121
STATS LOCAL FORWARD   -3.4237  0.73121
HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
            m->m     m->i     m->d     i->m     i->i     d->m     d->d
  COMPO   2.13250  4.16340  2.99229  3.02036  3.87184  2.21440  3.80529  2.76276  3.25697  2.05995  3.61528  3.06644  3.81269  3.47054  3.36166  2.55389  2.94438  2.79865  5.94288  3.49720
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
          0.00026  8.64427  9.36662  0.61958  0.77255  0.00000        *
      1   1.46753  8.28537  9.08330  9.14614  9.29530  0.65366  9.44329  8.83078  8.94404  8.52503  4.71174  3.07625  7.98521  8.93162  8.80150  2.07125  2.99882  4.10149 10.63242  9.68686      1 G - - H

also how do I get all pfam family HMM profiles in one file?

 

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Medhat8.0k
$ wget "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"

$ gunzip Pfam-A.hmm.gz

Keep all ids in a file called key, then do

$ hmmfetch -f -o key_hmm Pfam-A.hmm key

The file key_hmm contains all the HMM profiles of your ids.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by venu5.7k

Does the Pfam-A.hhm need to be indexed with hmmindex nefore? I cannot get hfetch work!!
 

ADD REPLYlink written 3.6 years ago by dago2.5k
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