Sequence aligment of short nucleotide sequences

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VinBio's picture
Sequence aligment of short nucleotide sequences

Dear All,
I have to check homology of short amino acid sequences (about 20 to 50 residues) ... there are around 300 of them.
I want to compare their homology, as in how many a.a are common/ conserved, how many possessing essential amino acids, etc...
I tried using Bioedit software for aligning those sequences.. but the alignment is'nt working..!

Could you please suggest any other software/program for comparing such short peptide sequences?
Or is there any other approach for doing it?

Biju's picture
Hi Vin Bio

Hi Vin Bio
You could use BLASTn program from NCBI site for the purpose. I have used it for finding the sequence conservation across species in a short nucleotide sequence of 15-20 nucleotides. I t was vey user friendly.
Hope this helps.Good luck.
Biju Joseph

VinBio's picture
Thanks Biju for your reply..

Thanks Biju for your reply..
but mine are not nucleotide seq. they are amino acid short seqs. ... sorry abt the wrong 'title' i mistakenly put nucleotide instead of amino acid.
I did blastp for one of the seq. gave few similarities but then how to go abt for comparision of similarties.
I have to it for all 300 amino acid sequences/
can you kindly elaborate on that...


cupton's picture
Have you tried MUSCLE?http:/

Have you tried MUSCLE?

I'm not sure if our alignment editor will work with 300 proteins, you could try.

Nikail Collins
Nikail Collins's picture
MEGA for alignment

I use MEGA for most of my alignments.  Always make sure sequences are going in the correct direction meaning they are all going in the same direction or you will not get correct alignment.  Also, you could try aligning the more similar samples/segments first and then add on to the alignment so that you can see when and where the alignment "isn't working".