Retrieve data from one file comparing the ID in the second file Post: 302702177

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Top Forums Shell Programming and Scripting Retrieve data from one file comparing the ID in the second file Post 302702177 by kaav06 on Tuesday 18th of September 2012 03:41:44 AM

09-18-2012

Registered User

Retrieve data from one file comparing the ID in the second file

Hi all,

I have one file with IDs

Code:

Q8NDM7
P0C1S8
Q8TF30
Q9BRP8
O00258
Q6AWC2
Q9ULE0
Q702N8
A4UGR9
Q13426
Q6P2D8
Q9ULM3
A8MXQ7

I want to compare ID file with another file which has complete information about these IDs and also about other IDs which are not in the above ID file. As a result I want only information about the entries in the ID file. The second file has information such as

Code:

ID   3BP5L_HUMAN             Reviewed;         393 AA.
AC   Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3;
DT   05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2004, sequence version 1.
DT   05-SEP-2012, entry version 71.
DE   RecName: Full=SH3 domain-binding protein 5-like;
DE            Short=SH3BP-5-like;
GN   Name=SH3BP5L; Synonyms=KIAA1720; ORFNames=UNQ2766/PRO7133;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Brain;
RX   MEDLINE=21082932; PubMed=11214970; DOI=10.1093/dnares/7.6.347;
RA   Nagase T., Kikuno R., Hattori A., Kondo Y., Okumura K., Ohara O.;
RT   "Prediction of the coding sequences of unidentified human genes. XIX.
RT   The complete sequences of 100 new cDNA clones from brain which code
RT   for large proteins in vitro.";
RL   DNA Res. 7:347-355(2000).
RN   [2] //

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LEARN ABOUT DEBIAN

clustalo

clustalo(1)							   USER COMMANDS						       clustalo(1)

NAME

       clustalo - General purpose multiple sequence alignment program for proteins

SYNOPSIS

       clustalo [-h]

DESCRIPTION

       Clustal-Omega  is a general purpose multiple sequence alignment (MSA) program for proteins. It produces high quality MSAs and is capable of
       handling data-sets of hundreds of thousands of sequences in reasonable time.

       In default mode, users give a file of sequences to be aligned and these are clustered to produce a guide tree and this is used to  guide  a
       "progressive alignment" of the sequences.  There are also facilities for aligning existing alignments to each other, aligning a sequence to
       an alignment and for using a hidden Markov model (HMM) to help guide an alignment of new sequences that are  homologous	to  the  sequences
       used to make the HMM.  This latter procedure is referred to as "external profile alignment" or EPA.

       Clustal-Omega  uses  HMMs  for  the alignment engine, based on the HHalign package from Johannes Soeding [1]. Guide trees are made using an
       enhanced version of mBed [2] which can cluster very large numbers of sequences in O(N*log(N)) time. Multiple  alignment	then  proceeds	by
       aligning larger and larger alignments using HHalign, following the clustering given by the guide tree.

       In  its	current  form  Clustal-Omega can only align protein sequences but not DNA/RNA sequences. It is envisioned that DNA/RNA will become
       available in a future version.

USAGE

       Tool usage is available in /usr/share/doc/clustalo/README.

DEVELOPMENT

       Headers and libraries are available in libclustalo-dev package.

CITING

       Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H,
	Remmert M, Soding J, Thompson JD, Higgins DG (2011).  Fast, scalable generation of high-quality protein multiple sequence alignments
	using Clustal Omega. Mol Syst Biol 7.

AUTHOR

       Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging

       Conway Institute UCD Dublin (clustalw (at) ucd.ie) - clustalo

version 1.0.3							 December 14, 2011						       clustalo(1)

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