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... (5 Replies)
Hello All - I am looking for help on how to solve a re-occuring problem. I have a file with certain sequences in it that need to be removed. The sequences are always different but the fix is always the same remove those sequences and leave the rest. Another team ID's the bad sequences and then I... (3 Replies)
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... (8 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
I have a fasta file as follows
>sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3
MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN
TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM
KGVTSTRVYERA
>sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
>H8V34IS02I59VP
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 Replies)
I could calculate the length of entire fasta sequences by following command,
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta
But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be... (14 Replies)
I have a fasta file as follows
>sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3
MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM
ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC
NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Hi,
I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below
test.fasta
>TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
LEARN ABOUT OSX
locale::codes::langvar
Locale::Codes::LangVar(3pm) Perl Programmers Reference Guide Locale::Codes::LangVar(3pm)NAME
Locale::Codes::LangVar - standard codes for language variation identification
SYNOPSIS
use Locale::Codes::LangVar;
$lvar = code2langvar('acm'); # $lvar gets 'Mesopotamian Arabic'
$code = langvar2code('Mesopotamian Arabic'); # $code gets 'acm'
@codes = all_langvar_codes();
@names = all_langvar_names();
DESCRIPTION
The "Locale::Codes::LangVar" module provides access to standard codes used for identifying language variations, such as those as defined in
the IANA language registry.
Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default IANA language
registry codes will be used.
SUPPORTED CODE SETS
There are several different code sets you can use for identifying language variations. A code set may be specified using either a name, or
a constant that is automatically exported by this module.
For example, the two are equivalent:
$lvar = code2langvar('en','alpha-2');
$lvar = code2langvar('en',LOCALE_CODE_ALPHA_2);
The codesets currently supported are:
alpha
This is the set of alphanumeric codes from the IANA language registry, such as 'arevela' for Eastern Armenian.
This code set is identified with the symbol "LOCALE_LANGVAR_ALPHA".
This is the default code set.
ROUTINES
code2langvar ( CODE [,CODESET] )
langvar2code ( NAME [,CODESET] )
langvar_code2code ( CODE ,CODESET ,CODESET2 )
all_langvar_codes ( [CODESET] )
all_langvar_names ( [CODESET] )
Locale::Codes::LangVar::rename_langvar ( CODE ,NEW_NAME [,CODESET] )
Locale::Codes::LangVar::add_langvar ( CODE ,NAME [,CODESET] )
Locale::Codes::LangVar::delete_langvar ( CODE [,CODESET] )
Locale::Codes::LangVar::add_langvar_alias ( NAME ,NEW_NAME )
Locale::Codes::LangVar::delete_langvar_alias ( NAME )
Locale::Codes::LangVar::rename_langvar_code ( CODE ,NEW_CODE [,CODESET] )
Locale::Codes::LangVar::add_langvar_code_alias ( CODE ,NEW_CODE [,CODESET] )
Locale::Codes::LangVar::delete_langvar_code_alias ( CODE [,CODESET] )
These routines are all documented in the Locale::Codes::API man page.
SEE ALSO
Locale::Codes
The Locale-Codes distribution.
Locale::Codes::API
The list of functions supported by this module.
http://www.iana.org/assignments/language-subtag-registry
The IANA language subtag registry.
AUTHOR
See Locale::Codes for full author history.
Currently maintained by Sullivan Beck (sbeck@cpan.org).
COPYRIGHT
Copyright (c) 2011-2012 Sullivan Beck
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
perl v5.16.2 2012-10-11 Locale::Codes::LangVar(3pm)