Sequence Alignment of short amino acid sequences

[VinBio]

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..unable to draw any interpretation!

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

[sing09]

Let me see if I understand you. You would like to align the sequences against each other, correct? Use blastp: http://blast.ncbi.nlm.nih.gov/Blast.cgi ... LAST_INIT=

Check the box "Align two or more sequences" and follow instructions (question mark sign just beside it).

Hope this helps,

[VinBio]

Thanks Sing...
Yes u r right..I want to align them all to see their homology.
I tried doing blastp, but its automatically taking the first sequence as query and rest others as subject sequences!? ...
So do I need to go one by one everytime.. like take one sequence of the 300 sequences at a time and blast it with other 299..
that seems very time consuming.. is there any other way for doing that.. Please help

[VinBio]

Hi again.. Is it appropriate to use Mega4 software for the alignment?
I haven't used it before..but its available

[sing09]

Oh, I see. I do not recall aligning sequences without a query sequence, but I know you can paste more than one sequence in the query box. Do not use the "align 2 or more sequences" choice and try using just the query box. Your sequences need to be pasted in Fasta format one after another, just with the title separating them from each other.
I have never used the Mega4 software, sorry.
Let me know how it goes. I hope it works.

[VinBio]

Thanx Sing...
I tried doing that without checking the align two or more seqs. box.. but its automatically aligning 1st seq. with all ..then the second ..so on..

I tried using Mega4.. it does align all the sequence together and there is specific color for each type of a.a... thats good
But there are 300 sequences so there is hardly any similarity commonly seen in them..as the difference increases..
...u can even create a phylogenetic tree with this software.. its freely available on net

have a great day

[sing09]

I just took a look at Mega4. It seems to be a very comprehensive program for sequence analysis. I'll keep the information. Thanks and sorry for not being able to help much.

[bcwsaf]

ClustalW does a decent job of aligning multiple sequences. It's available at numerous websites, including the Baylor College of Medicine Search Launcher (http://searchlauncher.bcm.tmc.edu/), which also has lots of other useful sequence analysis utilities. If you then paste the resulting alignment into Boxshade (http://www.ch.embnet.org/software/BOX_form.html) you can choose various output formats, and whether to assign a consensus sequence or not. I don't recall whether you include the ClustalW alignment header information when you paste into Boxshade, but try with and without and one should work. You have to set the Input to "Other", then play around with the different output choices to see which ones work (some don't work for me), and which format you like the look of. I think I liked the RTFnew format, but it's been a while. Good luck.