Ronald Robertson

Sanjay Singh

Scientist/Writer
  • Emailsanjaysingh765@gmail.com
  • Socail@lampatlex
  • VisitorSince 1982
  • LocationKentucky, USA



Perl Script 5 : How to add specific word to fasta header

Question : I have more than 5000 fasta sequence in a file and want to add a word , for instance phosphate, to header of all sequence. please tell me a PERL solution for that.





Convert Multi Fasta file into a Single line FASTA File

Store Multi Fasta Header into a Separate File







Answer : So you have a file with multiline fasta file with several hundreads of sequence like this 

>Cryptococcus gattii

MGIKGLTGLLSENAPKCMKDHEMKTLFGRKVAIDASMSIYQFLIAVRQQDGQMLMNESGDVTSHLMGFFYRTIRMVDHGIKPCYIFDGKPPELKGSVLAKRFARREEAKEGEEEAKETGTAEDVDKLARRQVRVTREHNEECKKLLSLMGIPVVTAPGEAEAQCAELARAGKVYAAGSEDMDTLTFHSPILLRHLTFSEAKK

>Daphnia pulex

MGIKGLTQVIGDTAPTAIKENEIKNYFGRKVAIDASMSIYQFLIAVRSEGAMLTSADGETTSHLMGIFYRTIRMVDNGIKPVYVFDGKPPDMKGGELTKRAEKREEASKQLVLATDAGDAVEMEKMNKRLVKVNKGHTDECKQLLTLMGIPYVEAPCEAEAQCAALVKAGKVYATATEDMDSLTFGSNVLLRYLTYSEAKKM
and want to make them look like this



>Cryptococcus gattii - phosphate

MGIKGLTGLLSENAPKCMKDHEMKTLFGRKVAIDASMSIYQFLIAVRQQDGQMLMNESGDVTSHLMGFFYRTIRMVDHGIKPCYIFDGKPPELKGSVLAKRFARREEAKEGEEEAKETGTAEDVDKLARRQVRVTREHNEECKKLLSLMGIPVVTAPGEAEAQCAELARAGKVYAAGSEDMDTLTFHSPILLRHLTFSEAKK

>Daphnia pulex - phosphate

MGIKGLTQVIGDTAPTAIKENEIKNYFGRKVAIDASMSIYQFLIAVRSEGAMLTSADGETTSHLMGIFYRTIRMVDNGIKPVYVFDGKPPDMKGGELTKRAEKREEASKQLVLATDAGDAVEMEKMNKRLVKVNKGHTDECKQLLTLMGIPYVEAPCEAEAQCAALVKAGKVYATATEDMDSLTFGSNVLLRYLTYSEAKKM


this PERL one liner can help you





perl -p -e "s/^(>.*)$/$1-phosphate/g" input.fasta > out.fasta


where

phosphate - word you want to add

input.fasta - file where sequences are stored at present

out.fasta - file where your result will be stored





Comments

design

Onboarding Motivation

Onboarding Motivation
branding

Delivery App Wireframe

Delivery App Wireframe
creative

Guest App Walkthrough Screens

Guest App Walkthrough Screens
art

Project Managment Illustration

Project Managment Illustration
Photography

Photography

Lorem ipsum dolor sit amet consectetuer adipiscing elit aenean commodo ligula eget.

Web Development

Web Development

Lorem ipsum dolor sit amet consectetuer adipiscing elit aenean commodo ligula eget.

UI/UX design

UI/UX design

Lorem ipsum dolor sit amet consectetuer adipiscing elit aenean commodo ligula eget.

Sanjay Singh

Sanjay Singh

I am lexicographer

I'm a Scientist with 20+ years of broad experience in molecular biology and bioinformatics. Extensive experience in the regulation of metabolic pathways in plants. Proven success in the design, development, and deployment of several result-oriented research projects. Have worked with both academic and industrial collaborators.

Get in touch

Let's talk about everything!

Don't like forms? Send me an email. 👋

Experience

2019 - Present

Acamedic Degree

Lorem ipsum dolor sit amet quo ei simul congue exerci ad nec admodum perfecto.

2017 - 2013

Bachelor’s Degree

Lorem ipsum dolor sit amet quo ei simul congue exerci ad nec admodum perfecto.

2013 - 2009

Honours Degree

Lorem ipsum dolor sit amet quo ei simul congue exerci ad nec admodum perfecto.

2019 - Present

Web Designer

Lorem ipsum dolor sit amet quo ei simul congue exerci ad nec admodum perfecto.

2017 - 2013

Front-End Developer

Lorem ipsum dolor sit amet quo ei simul congue exerci ad nec admodum perfecto.

2013 - 2009

Back-End Developer

Lorem ipsum dolor sit amet quo ei simul congue exerci ad nec admodum perfecto.