Multiple Sequence Alignment

Regardless of the outcome of your searches, you will want a multiple sequence alignment containing your sequence and all the homologues you have found above.

Some sites for performing multiple alignment:

If you are going to do a lot of alignments, then it is probably best to get your own copy of one of many programs, some FTP sites for some of these are:

Note that PileUp is contained within the GCG commercial package. Most institutions with people doing this sort of work will have access to this software, so ask around if you want to use it.

Probably the most important advance since these pages first appeared are Hidden Markov Models for sequence alignment. Several methods are listed above.

Alignments can provide:

Some tips

Next secondary structure prediction.

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