Shell script for changing the accession number of DNA sequences in a FASTA file Post: 302881551

10 More Discussions You Might Find Interesting

1. 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...

2. UNIX for Dummies Questions & Answers

trying to grep -v multiple changing sequences from a file

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. 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...

4. Shell Programming and Scripting

Extract sequences from a FASTA file based on another file

5. Shell Programming and Scripting

Shorten header of protein sequences in fasta file

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...

6. UNIX for Dummies Questions & Answers

Select distinct sequences from fasta file and list

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...

7. Shell Programming and Scripting

Getting unique sequences from multiple fasta file

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...

8. UNIX for Beginners Questions & Answers

How to count the length of fasta sequences?

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...

9. Shell Programming and Scripting

Shorten header of protein sequences in fasta file to only organism name

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...

10. UNIX for Beginners Questions & Answers

How to add specific bases at the beginning and ending of all the fasta sequences?

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...

LEARN ABOUT DEBIAN

clustalo

clustalo(1)							   USER COMMANDS						       clustalo(1)

NAME

       clustalo - General purpose multiple sequence alignment program for proteins

SYNOPSIS

       clustalo [-h]

DESCRIPTION

       Clustal-Omega  is a general purpose multiple sequence alignment (MSA) program for proteins. It produces high quality MSAs and is capable of
       handling data-sets of hundreds of thousands of sequences in reasonable time.

       In default mode, users give a file of sequences to be aligned and these are clustered to produce a guide tree and this is used to  guide  a
       "progressive alignment" of the sequences.  There are also facilities for aligning existing alignments to each other, aligning a sequence to
       an alignment and for using a hidden Markov model (HMM) to help guide an alignment of new sequences that are  homologous	to  the  sequences
       used to make the HMM.  This latter procedure is referred to as "external profile alignment" or EPA.

       Clustal-Omega  uses  HMMs  for  the alignment engine, based on the HHalign package from Johannes Soeding [1]. Guide trees are made using an
       enhanced version of mBed [2] which can cluster very large numbers of sequences in O(N*log(N)) time. Multiple  alignment	then  proceeds	by
       aligning larger and larger alignments using HHalign, following the clustering given by the guide tree.

       In  its	current  form  Clustal-Omega can only align protein sequences but not DNA/RNA sequences. It is envisioned that DNA/RNA will become
       available in a future version.

USAGE

       Tool usage is available in /usr/share/doc/clustalo/README.

DEVELOPMENT

       Headers and libraries are available in libclustalo-dev package.

CITING

       Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H,
	Remmert M, Soding J, Thompson JD, Higgins DG (2011).  Fast, scalable generation of high-quality protein multiple sequence alignments
	using Clustal Omega. Mol Syst Biol 7.

AUTHOR

       Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging

       Conway Institute UCD Dublin (clustalw (at) ucd.ie) - clustalo

version 1.0.3							 December 14, 2011						       clustalo(1)