August 22, 2012 at 1:51 pm #16770
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.
August 22, 2012 at 2:46 pm #112136JackBeanParticipant
So I’m away from computer and I want to do pairwise alignment?
August 22, 2012 at 3:50 pm #112138
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
August 22, 2012 at 9:48 pm #112146JackBeanParticipant
I see. So I will probably click 1500 nucleotides one by one, right?
August 22, 2012 at 11:45 pm #112147
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!
September 17, 2012 at 2:13 am #112371
Hope you will find it useful!
July 16, 2013 at 2:35 am #114090jeffzParticipant
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.
July 31, 2013 at 12:17 pm #114129sullivanParticipant
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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