How To Do Alignment Between Seqres And Atom Sequences From Scop Using Biopython Or With R?

Question

[Lakshmi]

Hi,

I am trying to do an alignment between seqres and seqatom sequences from SCOP database. How to do this with Biopython or with R? Is there any other methods available for getting this alignment?

I had asked this question two days ago. But Mr.neilfws closed as duplicate.I didn't understand why he closed my question? I Would like to get answers from Biostar community.

[Neilfws]

The question was closed as a duplicate because there's an existing question which is very similar, with an accepted answer - http://biostar.stackexchange.com/questions/13526/multiple-sequence-alignment-in-biopython. When questions are closed as duplicates, the link to the duplicate appears above the question. If you believe that your question is different to that one, make your case using the "add comment" link under this question. Otherwise, I'll close it again.

[Jan Kosinski]

Lakshmi, maybe my new answer (the old one was not fully correct) for the old question would match your needs. Please note that both questions ask for the the same thing: mapping of seqres to atom, so your question should be closed unless your specific aim is provided.

[Lakshmi]

My question is somewhat similar from that question but I can't accept that answer.My aim of the work is different from that one. I am looking for other methods and suggestions. If you know anything about this question, please give suggestions.

Answer 1

[dimkal]

not sure if this will be useful, but you can get the structure-implied sequence alignment from Homstrad (http://tardis.nibio.go.jp/homstrad) database. The sequences are then manually curated for accuracy for most SCOP families.