SELEX multiple alignment format

From BioPerl

Description

SELEX is an interleaved multiple alignment format that arose as an intuitive format, easy to write and manipulate manually with a text editor. It is usually easy to convert other alignment formats into SELEX format (though it can be harder to go the other way, since SELEX is more free-format than other alignment formats). For instance, GCG's MSF multiple alignment format and the output of the CLUSTALV multiple alignment program are similar interleaved formats. Because SELEX evolved to accomodate different user input styles, it is very tolerant of various inconsistencies such as different gap symbols, varying line lengths, etc.

SELEX format is used by Sean Eddy's HMMER package. It can store RNA secondary structure as part of the sequence annotation.

Example

# Example selex file

seq1     ACGACGACGACG.
seq2     ..GGGAAAGG.GA
seq3     UUU..AAAUUU.A

seq1  ..ACG
seq2  AAGGG
seq3  AA...UUU

Finding DNA or RNA ligands

Systematic Evolution of Ligands by EXponential Enrichment is also a method for selecting nucleic acids with specific binding properties, see All you wanted to know about SELEX...