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Android app for Pairwise Protein Alignment

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Android app for Pairwise Protein Alignment

Postby deeptakverma » Wed Aug 22, 2012 1:51 pm

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.
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Postby JackBean » Wed Aug 22, 2012 2:46 pm

So I'm away from computer and I want to do pairwise alignment?
http://www.biolib.cz/en/main/

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Re: Android app for Pairwise Protein Alignment

Postby deeptakverma » Wed Aug 22, 2012 3:50 pm

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
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Postby JackBean » Wed Aug 22, 2012 9:48 pm

I see. So I will probably click 1500 nucleotides one by one, right?
http://www.biolib.cz/en/main/

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Re: Android app for Pairwise Protein Alignment

Postby deeptakverma » Wed Aug 22, 2012 11:45 pm

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!
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Re: Android app for Pairwise Protein Alignment

Postby deeptakverma » Mon Sep 17, 2012 2:13 am

Thanks davidflora.
Hope you will find it useful!
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Postby jeffz » Tue Jul 16, 2013 2:35 am

I knew that android has gone too far in developing apps for almost apps for every field of life. And by checking your link I am more impressed buddy. I have not tried yet but i hope that this app will be very helpful.
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Re: Android app for Pairwise Protein Alignment

Postby sullivan » Wed Jul 31, 2013 12:17 pm

This system utilization the Needleman–wunsch and Smith–waterman calculations for pairwise protein worldwide and nearby arrangement, separately. The successions might be entered in three diverse routes: series of characters, NCBI promotion number or PDB ID.
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