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Comparison between two peptide sequences!

  1. Oct 11, 2004 #1
    hello everybody!

    i have to find match between two different peptide sequences (looking for related sequences), but don't know where and how i can do it. i have very little bioinformatic background.

    i hope for some help.

    thanks alot!
     
  2. jcsd
  3. Oct 11, 2004 #2

    iansmith

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    To compare 2 sequences you can use "BLAST 2 Sequence" from NCBI
    http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html

    You will have to select BLASTP as a program nand just have to paste your sequence in the respective box.

    If you want something a more effecient or want to compare more than 2 sequences, I suggest that you use a program called CLUSTAL.

    You can access a version of CLUSTAL at the Biology Workbench from UCSD
    http://workbench.sdsc.edu/
    You will have to register. This website also has several other bioinformatic tool.
     
  4. Oct 11, 2004 #3
    Sorry for chiming in unexpectedly. I remember my gal studying about algorithms on bioinformatics, she once said she also wanted to write algorithms, make applications about sequence matching. Are those apps as in the links you posted the same as what my gal has been doing ? Thank you

    Edit to plus: I am not biologist or computer sceintist, medon't know,please be kind to tell me?
     
    Last edited: Oct 11, 2004
  5. Oct 11, 2004 #4
    thanks! i will check it.
     
  6. Oct 11, 2004 #5

    iansmith

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    It probably the same kind of programming
     
  7. Oct 11, 2004 #6
    :wink: your so sweet, I will delve into them, sort of changing my major, :biggrin:
     
  8. Oct 13, 2004 #7

    hello Ian!

    now i want to align more than two protein sequences but can't find the CRUSTAL program you talked about. they have CRYSTALDIST, CRYSTALTREE...but not CRYSTAL :eek: may you tell me why and how i can align more than two protein sequences?

    big thanks!
     
  9. Oct 13, 2004 #8

    iansmith

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    Do not go into the aligment tool section, you have to go into the nucleic or protein tool depending on what you are using. Then you select "add new sequence" and click run to add all the sequence you want to use. You will then have a list of sequences. You then select (check the box beside the name) the sequence you added, select "CLUSTALW - multiple sequence alignment" and click run. You are then taken to a new screen with option for the program. I usually do not change anything the default option are fine. You may want to change the "Guide tree display" from "unrooted" to "unrooted and rooted". When you are finished click "Submit". It may take a while but will have the alignment.
     
  10. Oct 13, 2004 #9
    hi Ian!

    thanks! :rofl:

    yeah, i think i have got the alignment :biggrin: but how do i label my sequence (workbench label) ? and besides is there a place i can learn how to use these program? i feel like drowning in all the infos...totally lost!


    BTW what does they mean with:
    - single, fully conserved residue.
    - conservation of strong groups.
    - conservation of weak groups.


    what exactly is residue is that amino acid?, strong groups? and weak group?

    i have clicked on "Help" button, but it doesn't give me any good help.
    thanks!
     
    Last edited: Oct 13, 2004
  11. Oct 13, 2004 #10

    iansmith

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    To add a label, you have to write a title in the name box when you add a sequence. You can also replace the label by editing the sequence.

    As far as for learning these program, you might have to take a bioinformatic course. To learn more about the program you can click on them then press "Help" to get all the information.
     
  12. Oct 13, 2004 #11
    hi Ian!

    thanks for your patience!

    but from my alignment result i got these terms:

    - single, fully conserved residue.
    - conservation of strong groups.
    - conservation of weak groups.

    what does it mean with strong groups and weak group? i have not heard about them before. residue must be amino acid though.

    i have clicked on "Help" button, but it doesn't give me any good help.

    thanks!
     
  13. Oct 13, 2004 #12

    iansmith

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    A residue is the amino acid. A strong group is a group of amino acid that share almost characteristic and any amino acid from this group will may have a significant effect on the protein. A weak group is group that share a limited number of characteriste and this will have some significant but limited effect on the protein.
     
  14. Oct 13, 2004 #13
    thanks! :smile:
     
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