Hello all,

Today’s is a short assignment highlighting some of the multiple sequence alignment techniques that we discussed on Monday’s lecture.  Expect to work through this exercise during the first hour or so of today’s class, following which we will discuss the results as a group.

Assignment #7: MCB_5472_Assignment_7 (pdf) MCB_5472_Assignment_7 (docx)

Lecture: MCB5472_Assignment_7_lecture_Mar-5-14 (pptx) MCB5472_Assignment_7_lecture_Mar-5-14 (pdf)

The multiple sequence file that you will use as input is: BALiBASE3_faa

The corresponding reference alignment for these sequences is: BALiBASE3_msf

“.msf” files are a common multiple sequence alignment format. You can use that handy “seqret” program to convert this format into something else (and vice versa) see: http://emboss.open-bio.org/rel/dev/apps/seqret.html.  All of the multiple sequence programs that we will use in this exercise output aligned multiple fasta files by default, and these can also be read by most alignment viewers.

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