Android app for Pairwise Protein Alignment

[deeptakverma]

This android app uses the Needleman–Wunsch and Smith–Waterman algorithms for pairwise protein global and local alignment, respectively. Very useful when you are away from computer.

The sequences can be entered in three different ways:
1. string of characters
2. NCBI accession number
3. PDB ID
4. or in any combination of the above

The program can also generate a dot plot for the alignment.

The app is freely available on google app market.
Here's the link: https://play.google.com/store/search?q= ... ner&c=apps

Hope this helps all biologists / bioinformaticians working with proteins and protein sequences.

[JackBean]

So I'm away from computer and I want to do pairwise alignment?

[deeptakverma]

Exactly!

You can either enter you own amino acid sequences for alignment or...

if you just enter PDBID or protein NCBI accession ID, the app automatically fetches the protein sequence from the database and aligns them.

Other features of the app:
Gap penalties: Open, Affine and Extension penalties
Substitution matrices: Blosum60, PAM250, Gonnet250, etc

[JackBean]

I see. So I will probably click 1500 nucleotides one by one, right?

[deeptakverma]

In my previous post, I wrote:

"if you just enter PDBID or protein NCBI accession ID, the app automatically fetches the protein sequence from the database and aligns them."

Every sequence in the database has a unique identifier. You only need to enter that identifier and the app will fetch the sequence on its own.

For example: Lysozyme protein has 130 amino acids (or characters). You wouldn't want to type-in all those characters. But since, lysozyme's PDBID is "1LZ1" ... if you just enter this ID... the app will fetch 130 sequences. Easy!

[deeptakverma]

Thanks davidflora.
Hope you will find it useful!