SELEX multiple alignment format
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
#=SQ HSFAU 1.00 - - 0..0:0 H.sapiens fau mRNA #=SQ HSFAU1 1.00 - - 0..0:0 H.sapiens fau 1 gene HSFAU ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc HSFAU1 ctaccattttccctctcgattctatatgtacactcgggacaagttctcct HSFAU gccaatatgcagctctttgtccgcgcccaggagctacacaccttcgaggt HSFAU1 gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg HSFAU gaccggccaggaaacggtcgcccagatcaaggctcatgtagcctcactgg HSFAU1 gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc HSFAU agggcattgccccggaagatcaagtcgtgctcctggcaggcgcgcccctg HSFAU1 tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac HSFAU gaggatgaggccactctgggccagtgcggggtggaggccctgactaccct HSFAU1 accggttctccatccccgcagcgtagcccggaacatggtagctgccatct HSFAU ggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc HSFAU1 ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgccccg HSFAU gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaag HSFAU1 tcctgcgcgagctgctgcccaggcaggttcgccggtgcgagcgtaaaggg HSFAU aagaagaagaagacaggtcgggctaagcggcggatgcagtacaaccggcg HSFAU1 gcggagctaggactgccttgggcggtacaaatagcagggaaccgcgcggt HSFAU ctttgtcaacgttgtgcccacctttggcaagaagaagggccccaatgcca HSFAU1 cgctcagcagtgacgtgacacgcagcccacggtctgtactgacgcgccct HSFAU actcttaagtcttttgtaattctggctttctctaataaaaaagccactta HSFAU1 cgcttcttcctctttctcgactccatcttcgcggtagctgggaccgccgt HSFAU gttcagtcaaaaaaaaaa HSFAU1 tcaggtaagaatggggccttggctggatccgaagggcttgtagcaggttg HSFAU HSFAU1 gctgcggggtcagaaggcgcggggggaaccgaagaacggggcctgctccg HSFAU HSFAU1 tggccctgctccagtccctatccgaactccttgggaggcactggccttcc HSFAU HSFAU1 gcacgtgagccgccgcgaccaccatcccgtcgcgatcgtttctggaccgc HSFAU HSFAU1 tttccactcccaaatctcctttatcccagagcatttcttggcttctctta HSFAU HSFAU1 caagccgtcttttctttactcagtcgccaatatgcagctctttgtccgcg HSFAU HSFAU1 cccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcccag HSFAU HSFAU1 atcaaggtaaggctgcttggtgcgccctgggttccattttcttgtgctct HSFAU HSFAU1 tcactctcgcggcccgagggaacgcttacgagccttatctttccctgtag HSFAU HSFAU1 gctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgct HSFAU HSFAU1 cctggcaggcgcgcccctggaggatgaggccactctgggccagtgcgggg HSFAU HSFAU1 tggaggccctgactaccctggaagtagcaggccgcatgcttggaggtgag HSFAU HSFAU1 tgagagaggaatgttctttgaagtaccggtaagcgtctagtgagtgtggg HSFAU HSFAU1 gtgcatagtcctgacagctgagtgtcacacctatggtaatagagtacttc HSFAU HSFAU1 tcactgtcttcagttcagagtgattcttcctgtttacatccctcatgttg HSFAU HSFAU1 aacacagacgtccatgggagactgagccagagtgtagttgtatttcagtc HSFAU HSFAU1 acatcacgagatcctagtctggttatcagcttccacactaaaaattaggt HSFAU HSFAU1 cagaccaggccccaaagtgctctataaattagaagctggaagatcctgaa HSFAU HSFAU1 atgaaacttaagatttcaaggtcaaatatctgcaactttgttctcattac HSFAU HSFAU1 ctattgggcgcagcttctctttaaaggcttgaattgagaaaagaggggtt HSFAU HSFAU1 ctgctgggtggcaccttcttgctcttacctgctggtgccttcctttccca HSFAU HSFAU1 ctacaggtaaagtccatggttccctggcccgtgctggaaaagtgagaggt HSFAU HSFAU1 cagactcctaaggtgagtgagagtattagtggtcatggtgttaggacttt HSFAU HSFAU1 ttttcctttcacagctaaaccaagtccctgggctcttactcggtttgcct HSFAU HSFAU1 tctccctccctggagatgagcctgagggaagggatgctaggtgtggaaga HSFAU HSFAU1 caggaaccagggcctgattaaccttcccttctccaggtggccaaacagga HSFAU HSFAU1 gaagaagaagaagaagacaggtcgggctaagcggcggatgcagtacaacc HSFAU HSFAU1 ggcgctttgtcaacgttgtgcccacctttggcaagaagaagggccccaat HSFAU HSFAU1 gccaactcttaagtcttttgtaattctggctttctctaataaaaaagcca HSFAU HSFAU1 cttagttcagtcatcgcattgtttcatctttacttgcaaggcctcaggga HSFAU HSFAU1 gaggtgtgcttctcgg
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...
