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.
#=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
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…