I have several sequences 30-60 Kbp and I want to recognized a conserved area, I used clustal omega, blast and other software but all of the hanged! I think that because of large size of my sequences, so I need to know if there are any other software (muscle not worked to).
Have you checked mafft? http://mafft.cbrc.jp/alignment/software/
In my experience this aligner has given to me the best results. In that link it is explained how to use it when the number of sequences is high.
Another option is AVID: http://genome.cshlp.org/content/13/1/97.long
which is an aligner designed for working with long sequences.
Hope that helps.
I think it is important to know how long you expect the conserved area to be, whether you expect it to be present only once in each sequence and whether you expect it to be positioned in a similar way. For example if the "conserved sequences" occur only as multiple short motifs at seemingly random positions, multiple alignment will not be the best approach and you could look into motif-finding software like MEME (http://meme-suite.org/).
If you already know what the conserved area is in at least one of the sequences, you can also try pairwise sequence alignment of all the other sequences against this particular one, which is computationally simpler than generating a multiple alignment.
Thanks Matej, this is very interested point. The question hear is how can us identify un-known phage i.e. the phage from environmental sample using molecular methods? if we proposed that we identify it morphologically. Does we have to design new primer for each one in each time? or there is other protocol?
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