Re: [R] Parsing protein sequences

From: S Peri <biocperi_at_yahoo.com>
Date: Thu 08 Jul 2004 - 23:56:01 EST


Dear All,
  I have two files with peptide sequences. These two have peptide sequences(obtained from tryptic and semi-tryptic digestion using Mass spec analysis). There are two columns :peptide sequence and protein name.  

File 2 has both tryptic and semi-tryptic peptides and File 1 has only semi-tryptic peptides. Is there a way out that I can filter semi-tryptic peptides from typtic ones. There are ~30,000 peptides in each file.

Please suggest if this can be done in R. I want to do further analysis involving some statistics using R.

Thank you in advance.
SP

File 1 (is a comma seperated file):

pepseq	 proteinname
FENGAFT	NP_065081.1
SLLEDIR	NP_062571.1
VCCEGMLIQ	NP_064583
NWGLSVYADKPETTK	NP_000598
MLAFDVNDEK	NP_000598


File 2 (comma seperated file):
SLLEDIR	NP_062571
TYMLAFDVNDEK	NP_000598
ASSLSESSPPK	NP_057441
LSIVVSLGTGR	NP_003551

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