As i am trying to do more work in Multiple sequence alignment using clustalw wrapper in biopython, i am wondering how can i pass parameters through clustalcommandline which i fail to do repeatedly.
Parameters in details like :
- Gap open penalty, Gap extension penalty, no end gap(yes, no), gap distance, weight matrix(blosum, pam etc), type (DNA,protein) and other optional parameters.
Right now i am working on default alignment settings provided by clustalw. As default settings are not fulfilling my interest, i am more keen in adding parameters in given below lines.
import sys, subprocess from Bio import AlignIO from Bio.Align.Applications import ClustalwCommandline cline = ClustalwCommandline("clustalw", infile="opuntia.fasta") child = subprocess.call(str(cline), shell=(sys.platform!="win32"))
Moreover, i will be more pleased if you guys will explain how can i know the inputted fasta file is of nucleotide,DNA or protein.
Thanks for your interest