How to count the length of fasta sequences? Post: 303033625

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Extract length wise sequences from fastq file

I have a fastq file from small RNA sequencing with sequence lengths between 15 - 30. I wanted to filter sequence lengths between 21-25 and write to another fastq file. how can i do that?

2. 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...

3. Shell Programming and Scripting

Extract sequences from a FASTA file based on another file

4. Shell Programming and Scripting

Count and search by sequence in multiple fasta file

Hello, I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table...

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. Shell Programming and Scripting

Outputting sequences based on length with sed

I have this file: >ID1 AA >ID2 TTTTTT >ID-3 AAAAAAAAA >ID4 TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC Add I am trying to use this script to output sequences longer than 15 characters: sed -r '/^>/N;{/^.{,15}$/d}' The desire output would be this: >ID4...

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

probalign

PROBALIGN(1)							   User Commands						      PROBALIGN(1)

NAME

       probalign - Align sequences in MFAFILE(s) and print result to standard output

DESCRIPTION

       PROBALIGN  Version  1.4	(Nov 2010) aligns multiple protein sequences and prints to the standard output. Written by Satish Chikkagoudar and
       Usman Roshan using code from PROBCONS version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein).

       PROBALIGN 1.4 comes with ABSOLUTELY NO WARRANTY.  This is free software, and you are welcome to redistribute it under  certain  conditions.
       See the README file for details.

   Usage:
	      probalign [OPTION]... [MFAFILE]...

   Description:
	      Align sequences in MFAFILE(s) and print result to standard output

       -clustalw

	      use CLUSTALW output format instead of MFA

       -v, --verbose

	      report progress while aligning (default: off)

       -a, --alignment-order

	      print sequences in alignment order rather than input order (default: off)

       -T, -temperature

	      Sets the thermodynamic temperature parameter

	      (default: 5 (for protein data mode), 1 ( for nucleotide data mode)).

       -score_matrix, --score_matrix

	      Sets  the  type of scoring matrix used to calculate the posterior probabilities (default: gonnet_160, representing gonnet 160, refer
	      README for details)

       -go, --gap-open

	      This option can be used to specify the gap open parameter. The default for Gonnet 160 (protein) is 22 and nucleotide (simple matrix)
	      is 4.

       -ge, --gap-extension

	      This  option  can  be  used to specify the gap extension parameter. The default for Gonnet 160 (protein) is 1 and nucleotide (simple
	      matrix) is 0.25.

       -nuc

	      Specify this option to indicate that inputted sequences are nucleotide sequences

       -prot

	      Specify this option to indicate that inputted sequences are protein sequences [DEFAULT]

       -showPP

	      Outputs the posterior probabilities of alignment columns as a new sequence named Posterior Probabilities (The probability values are
	      scaled to be between integers between 0 and 9).

probalign 1.4							     May 2011							      PROBALIGN(1)