Bash commands (bioinformatics)

What commands to use to find out the length as well as the number of hits (count) of multifasta sequence in linux?

bash commands fasta sequence

• 927 views • link

written 5.5 years ago by deblinaroy164.1995 •

Have you searched the forum?

• 0 views • link

written 5.5 years ago by Joe

0 answers

No answers yet.

More posts like this

Remote BLASTx : Strain specific search.
written 1.9 years ago by Saransh •

Hi community, Greetings! I am using remote BLASTx on my Linux machine for some bacterial species (Few Nucleotide sequences in FASTA file format). Following is …
NGS Ubunut commands
written 3.9 years ago by danielsjim71 •

I'm struggling this the linux/shell commands for NGS. Any tips? What is the Linux code to calculate the total number of lines in the FASTQ …
How to find average read length and number of reads in a bam file using samtools in linux?
written 4.1 years ago by MobiusT •

How to find average read length and number of reads in a bam file using samtools in linux? I used first `samtools stats file.bam | …
blast short sequence with multiple N bases
written 4.5 years ago by Nicolas •

Hello! I am trying to find a promoter inside a genome ensamble, I have the promoter sequence GGTTGTNNNNNNNNNACAACC Whenever I try to find this sequences …
Get full output with hmmscan in bio3d
written 5.4 years ago by lessismore

Dear, i am using `bio3d` to scan an input set of sequences for PFAM profiles. For this i simply use this code test <- read.fasta("/home/test.fa") …
Best way to normalize occurance of a nucleotide subsequence
written 9.7 years ago by snamjoshi87 •

If I have a set of nucleotide sequences of varying lengths and I want to find the number of times a certain subsequences occurs for …
Select only sequences that align with X% of a query during blastp search
written 11.2 years ago by dago

I have a Multifasta file that I use as query in a blastp search against nr. I would like to set a lower threshold indicating …
Best bioinfo one-liners?
written 11.2 years ago by Manu Prestat

Whereas an infinity of efficient tools exists out there, it is sometimes still quicker for achieving simple tasks to execute a one linux command. I'm …
Finding Integrative and Conjutative Elements in genomes (ICE)
written 11.7 years ago by robjohn70000

Hi, I blasted my contig sequences against a database of [ICE][1], but not sure what other filtering parameters to use apart from E-value<1e-5 and percent …
Finding a sequence in a fasta file
written 12.2 years ago by mbk0asis

Hi, all! Yesterday, I downloaded a [human lncRNA fasta file][1] from Genecode to find out if my presumably-novel-lncRNA-sequence exists in the database. I tried to …