12-27-2019
Thank you Robin for your detailed explanation. Here, I would like to repeat my question in clear manner.
I have a multiple directories, say for example org1, org2, org3 ..... org100 and each directory having a file namely dnaG.fasta. I need to copy all the dnaG.fasta file from each directory and paste in another directory fastconcatg. Therefore, my script has to copy dnaG.fasta file from each directory, add prefix to the file name like 1_dnaG.fasta, 2_dnaG.fasta ..... 100_dnaG.fasta and paste into the fastconcatg folder.
Last edited by dineshkumarsrk; 12-27-2019 at 09:25 AM..
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LEARN ABOUT DEBIAN
kalign
KALIGN(1) Kalign User Manual KALIGN(1)
NAME
kalign - performs multiple alignment of biological sequences.
SYNOPSIS
kalign [infile.fasta] [outfile.fasta] [Options]
kalign [-i infile.fasta] [-o outfile.fasta] [Options]
kalign [< infile.fasta] [> outfile.fasta] [Options]
DESCRIPTION
Kalign is a command line tool to perform multiple alignment of biological sequences. It employs the Muth?Manber string-matching algorithm,
to improve both the accuracy and speed of the alignment. It uses global, progressive alignment approach, enriched by employing an
approximate string-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global
alignment.
OPTIONS
-s -gpo -gapopen -gap_open x
Gap open penalty .
-e -gpe -gap_ext -gapextension x
Gap extension penalty.
-t -tgpe -terminal_gap_extension_penalty x
Terminal gap penalties.
-m -bonus -matrix_bonus x
A constant added to the substitution matrix.
-c -sort <input, tree, gaps.>
The order in which the sequences appear in the output alignment.
-g -feature
Selects feature mode and specifies which features are to be used: e.g. all, maxplp, STRUCT, PFAM-A?
-same_feature_score
Score for aligning same features.
-diff_feature_score
Penalty for aligning different features.
-d -distance <wu, pair>
Distance method
-b -tree -guide-tree <nj, upgma>
Guide tree method.
-z -zcutoff
Parameter used in the wu-manber based distance calculation.
-i -in -input
Name of the input file.
-o -out -output
Name of the output file.
-a -gap_inc
Increases gap penalties depending on the number of existing gaps.
-f -format <fasta, msf, aln, clu, macsim>
The output format.
-q -quiet
Print nothing to STDERR. Read nothing from STDIN.
REFERENCES
o Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics
6:298
o Timo Lassmann, Oliver Frings and Erik L. L. Sonnhammer (2009) Kalign2: high-performance multiple alignment of protein and nucleotide
sequences allowing external features. Nucleic Acid Research 3:858?865.
AUTHORS
Timo Lassmann <timolassmann@gmail.com>
Upstream author of Kalign.
Charles Plessy <plessy@debian.org>
Wrote the manpage.
COPYRIGHT
Copyright (C) 2004, 2005, 2006, 2007, 2008 Timo Lassmann
Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the
Free Software Foundation.
This manual page was written by Charles Plessy <plessy@debian.org> for the Debian(TM) system (but may be used by others). Permission is
granted to copy, distribute and/or modify this document under the same terms as kalign itself.
On Debian systems, the complete text of the GNU General Public License version 2 can be found in /usr/share/common-licenses/GPL-2.
kalign 2.04 February 25, 2009 KALIGN(1)