Need help with nucleic acids alignments - (Oct/04/2005 )
hello again.
sorry i wasn't around for a long time but i had some problems with my server...
i found a sort of answer finally with the following links, but thanks anyway for your time and help.
For anyone who is interested or have the same problem with me:
http://bio.ifom-firc.it/BLAST/index.shtml
and
http://www.ebi.ac.uk/cgi-bin/clustalw/resu...465556&poll=yes
I'm confused -- I thought you wanted to compare each of the 50 or so sequences to each other, not to a database (so I'm not sure how the BLAST interface helps), and you wanted a way to do it all at once (so I'm not sure how Clustal helps).
I know Clustal will compare them all and make a multiple alignment, but I was under the impression that you needed similarity percentages and such, which Clustal doesn't do. I also know BLAST can do batch input -- but I use the stand-alone netblast client (blastcl3) from NCBI (see here).
You know, in thinking a bit more about this problem, you could use the NCBI command line utilities to transform your sequences into a blastable database, then use the blastcl3 client to blast each of them against that database...
In any event, I'm glad you got it sorted out!
Hello!
I have the following problem:
I have 50 nucleic acids sequences and i have to compare them all one by one.
Is there a program or something that can help do this without much trouble?
It's really painfull and time-consuming to compare them with the help of programs or webpages i now so far.
I hope someone can help me.
Thanks a lot!
Did you try this one?
You can do multiple sequence alignment at one step using the bioinformatics tool available at baylor college of medicine genomic web page
well, with the crystalW i did the following: it gives you the scores for each alignment, and from this one is really easy to find the % percentage. And then it also gives you a guide tree (phylogram) and so you can also have groups of all sequences. and that's really good. 
Afterwards, i went to this Blast server that i mentioned above and it did [all by it self! ] all the BLASTs at once, for each of my nucleotides!
I now it maybe sound stupid and maybe there were so many programs that do this but i didn't know! thanks for the help again!