Blog

26Aug

How to rename fasta headers according to a matching name list

FaBox  has several utilities to manipulate the FASTA sequence. I wanted to replace the FASTA header with the new header or description which...

14Sep

How Do I Install and Use Bioperl on Ubuntu 14.04.1 LTS

Bioperl is necessary to run several Perl script which can save your day. Although Perl already comes with Ubuntu but Bioperl should be insta...

06Feb

Learn PERL Basic with Me

I have decided to teach basics of PERL to myself. I believe that there are more people who are teaching themselves. So we can learn PERL tog...

23Jan

How to Get Accession Numbers from FASTA File from GenBank

Say if have retrieved multiple FASTA Sequences using Uniprot ID from Uniprot or NCBI and now you want to get the accession numbers from FA...

09Jul

How to Split Multi line FASTA Files with PERL Script

Recently someone anonymous (surprisingly most of the reader who comment on this blog are anonymous) asked for a PERL script to split a multi...

05Apr

How to retrieve NCBI GenBank records with a range of accession numbers

I have previously discussed the way to download the sequence from NCBI database if you have a list of accession numbers. But what if you h...

04Apr

How to Remove Duplicate Sequences from a multi fasta Files

Most common problems with sequence analysis is presence of duplicate sequence in data sets. Even protein or nucleotide sequences downloaded ...

12Mar

How to Extract FASTA Header With PERL Script

Previously I have already shared some tricks and PERL script to extract the FASTA header fro multi FASTA files. I am adding another PERL scr...

11Mar

How to Parse/Edit FASTA header

Imagine a situation that you have thousands of FASTA sequences in a file and want to shorten or edit the FASTA header instead of whole long ...

09Jul

Easiest Way to Install BIO PERL Module on Window

If you are a PERL lover and use different PERL scripts or BIOPERL modules , then it is very obvious that you may face the problem of missin...

08Mar

Perl Script 6: How to search NCBI database using PERL script

I was thinking that will not it be an exciting idea to search my favorite database NCBI right from my desktop. in search of solution of thi...

03Mar

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. pleas...

26Feb

How to install Bioperl in window 7

In our previous post, I have discussed that how to install PERL on window machines . So now you have PERL on you machines but want to instal...

26Feb

How to install Bioperl in window xp

Bioperl is a collection of modules which can be used in Perl for sequence data analysis. When you have installed ActiveState perl (in the pr...

16Feb

Perl Script 4: How to BLAST multiple sequences against NCBI database using PERL script

Have you ever thought about BLASTing your single/multiple sequences against NCBI database without going to their webpage? Sounds good!! OK, ...

10Feb

Perl Script 2 : Convert Multi Fasta file into a Single line FASTA File

Question :  Update : 7.11.18 You can also use AWK to solve this problem awk '/^>/ {printf("\n%s\n",$0);next; } { printf(&qu...

05Nov

Easiest Way to Run Perl Script on Windows

So you have installed the PERL interpreter on your Windows machine and want to check whether it's working properly or not. So in this   ...

02Nov

Easiest Way To Install Perl on Windows

We have already talked about how to get PERL fro free and Other software essential for PERL scripting. in t his Bioinformatics Video Tutoria...