Alignment software to compare huge number of peptide sequences or cysteine framework

[LucasVS]

Hi everyone !

I have to find sequence similarities and to align about 5,000 peptide sequences (from 10 to 60 amino acid length) coming from 2 different organisms.

These sequences have highly conserved Cysteine residues arranged in different but also conserved cystein frameworks.
(e.g:
xCxxxCCxxxCx = framework 1
xCxCxCx = framework 2
xCCxxxCxxCx = framework 3
etc.
where "C" = Cysteine, and "x" can be any amino acid excepted Cysteine)

So I would like to find a software in order to:
1st - Compare the entire sequences (with all the amino acids)
2nd - If I don't find sequence similarities, then I would like to compare only the cysteine frameworks (i.e position of cysteines to each other + length of inter-cysteine sequences), even if the amino acids between the cysteines are totally different.

I listed all these sequences in an Excel sheet, and I can easily convert them into a Fasta file if needed.
I also modified the sequences to display only the Cysteines as in the following example:
NNKYCCHLWCTKHPRC into ----CC---C-----C

PS:
- What about MacVector?
- Would it be possible to align the sequences directly in Excel if I find a formula or a script ?

Thanks in advance !
Cheers

[mfursov]

Originally Posted by LucasVS

Hi everyone !
So I would like to find a software in order to:
1st - Compare the entire sequences (with all the amino acids)
2nd - If I don't find sequence similarities, then I would like to compare only the cysteine frameworks (i.e position of cysteines to each other + length of inter-cysteine sequences), even if the amino acids between the cysteines are totally different.

A) Load all sequences as alignment in UGENE ([Only registered users see links. ])

B) Use MUSCLE or KAlign algorithms - these algorithms are very fast and will align your sequences in a seconds/minutes

C) Check the result. If you want to realign some core part of the alignment - just select it and realign this region only. You can also export the region you need and store it to file as a separate alignment

D) Check "Statistics" context menu item - it can help you to see the data in alternative way