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    • #16770
      deeptakverma
      Participant

      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.

    • #112136
      JackBean
      Participant

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

    • #112138
      deeptakverma
      Participant

      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

    • #112146
      JackBean
      Participant

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

    • #112147
      deeptakverma
      Participant

      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!

    • #112371
      deeptakverma
      Participant

      Thanks davidflora.
      Hope you will find it useful!

    • #114090
      jeffz
      Participant

      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.

    • #114129
      sullivan
      Participant

      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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