Convert a DNA sequence into Amino Acid Post: 302957627

9 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

escape sequence for $

Hi all, I have a requirement where the variable name starts with $, like $Amd=/home/student/test/ How to work wit it? can some one help me, am in gr8 confusion:confused:

2. Shell Programming and Scripting

How to remove those sequence with same amino acid?What command line I should type?

My input is listed as: giNumber RefAminoAcid VarAminoAcid 10190711 P P 10190711 D D 109255248 I A 110349771 A ...

3. Shell Programming and Scripting

Extracting DNA sequences from GenBank files using Perl

Hi all, Using Perl, I need to extract DNA bases from a GenBank file for a given plant species. A sample GenBank file is here... Nucleotide This is saved on my computer as NC_001666.gb. I also have a file that is saved on my computer as NC_001666.txt. This text file has a list of all...

4. Shell Programming and Scripting

Tricky task with DNA sequences.

I am trying to reverse and complement my DNA sequences. The file format is FASTA, something like this: Now, to reverse the sequence, I should start reading from right to left. At the same should be complemented. Thus, "A" should be read as "T"; "C" should be read as "G"; "T" should be converted...

5. Shell Programming and Scripting

find common entries and match the number with long sequence and cut that sequence in output

Hi all, I have a file like this 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. FT COILED 59 140 ...

6. Shell Programming and Scripting

How to convert multiple number ranges into sequence?

Looking for a simple way to convert ranges to a numerical sequence that would assign the original value of the range to the individual numbers that are on the range. Thank you given data 13196-13199 0 13200 4 13201 10 13202-13207 3 13208-13210 7 desired...

7. Shell Programming and Scripting

Sequence generator

Thanks Guys This really helped

8. Shell Programming and Scripting

Shell script for changing the accession number of DNA sequences in a FASTA file

Hi, I am having a file of dna sequences in fasta format which look like this: >admin_1_45 atatagcaga >admin_1_46 atatagcagaatatatat with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to...

9. Red Hat

Rm -rf * sequence

If I run rm -rf * command under one parent directory. /data > rm -rf * Is there anyway to know which files will be deleted first ? Start using code tags please, ty.

LEARN ABOUT LINUX

shtool-subst

SHTOOL-SUBST.TMP(1)					      GNU Portable Shell Tool					       SHTOOL-SUBST.TMP(1)

NAME

       shtool-subst - GNU shtool sed(1) substitution operations

SYNOPSIS

       shtool subst [-v|--verbose] [-t|--trace] [-n|--nop] [-w|--warning] [-q|--quiet] [-s|--stealth] [-i|--interactive] [-b|--backup ext]
       [-e|--exec cmd] [-f|--file cmd-file] [file] [file ...]

DESCRIPTION

       This command applies one or more sed(1) substitution operations to stdin or any number of files.

OPTIONS

       The following command line options are available.

       -v, --verbose
	   Display some processing information.

       -t, --trace
	   Enable the output of the essential shell commands which are executed.

       -n, --nop
	   No operation mode. Actual execution of the essential shell commands which would be executed is suppressed.

       -w, --warning
	   Show warning on substitution operation resulting in no content change on every file. The default is to show a warning on substitution
	   operations resulted in no content change on all files.

       -q, --quiet
	   Suppress warning on substitution operation resulting in no content change.

       -s, --stealth
	   Stealth operation. Preserve timestamp on file.

       -i, --interactive
	   Enter interactive mode where the user has to approve each operation.

       -b, --backup ext
	   Preserve backup of original file using file name extension ext.  Default is to overwrite the original file.

       -e, --exec cmd
	   Specify sed(1) command directly.

       -f, --file cmd-file
	   Read sed(1) command from file.

EXAMPLE

	#   shell script
	shtool subst -i -e 's;(c) ([0-9]*)-2000;(c) 1-2001;' *.[ch]

	#    RPM spec-file
	%install
	    shtool subst -v -n 
		-e 's;^(prefix=).*;1 $RPM_BUILD_ROOT%{_prefix};g' 
		-e 's;^(sysconfdir=).*;1 $RPM_BUILD_ROOT%{_prefix}/etc;g' 
		`find . -name Makefile -print`
	    make install

HISTORY

       The GNU shtool subst command was originally written by Ralf S.  Engelschall <rse@engelschall.com> in 2001 for GNU shtool.  It was prompted
       by the need to have a uniform and convenient patching frontend to sed(1) operations in the OpenPKG package specifications.

SEE ALSO

       shtool(1), sed(1).

18-Jul-2008							   shtool 2.0.8 					       SHTOOL-SUBST.TMP(1)