This program searchs transposons of Class II which are characterized by the existence of terminal inverted repeats, denoted TIR's, that flank the transposons. Then, given the TIR, the program finds all locations at which the direct and inverse TIR approximate matches the DNA sequence and whose distance lies within a given range. Finally TRANSPO returns the following five sequences:
This is an example of a DNA sequence written in GenBank format:
1 GGACAGCGGA ATCCTCGACC CGGTTGAGGA ATGGTCGACG AAAATCTATC GGGTTCGAGG
61 ATTCGTCGAC CAGGTGTTGG AATCGTCGAC CGAGTCTGAG AATTCGTAGA CCAGGACGGC
121 GGAATCCTCG ACAATGACGA GGTATGGTCG AGGAAAATCT ATCGGGTTCG AGGATTCGTC
181 TACCAGGTGA TGGAATCCTC GACCAGGACA AAGAATTCGT CGACCAGGGG TGGAATTGTT
241 GTTATTCCGA TCATGAGAGC GGATATCAGT ACAGATCCGA CGCTGGTGAA AAAGATCACG
301 GCGATCGTGG ATAGTATCAA GCCACCGAGA GTCTCGTATT CGGAGAAAGA TCGGCCGATG
361 AGGATAAGAG GTCGATCGGA TGGACGGAAG AGGTAGAGGA AGAGCCATGA AGCGGCGAGG
421 CATAGGAGGA GGATGAGCGA GAATGGGTGG GCGGGAAGAG AGAAACTGAT GATCAGAGCG
481 ATGATGCAGA CGTAATTCAC CCTGAAATAA GAGGAGTTCT TCCAGAATCG CGTCATGGCC
541 TCGAAGACAG AGTCAAGCTT GGTGAAAAGC AGATCGTTCG AGGAGCTCTG ACCACGGCCG
601 GCTACGAGAT AGACCACCAC GAACCGTCTT GGTCACACTG TTGACAAATG CATGGACGGT
661 TGGAGGTTGT GATTCCACCA CATCAGTTAC AATCGGAGGC TGATCCGGAC TTGGCTGTTG
721 CGGTGGTGGA AATCGGAAGC ACAGGGGGAT TTGTGGACAC CATTCGATTT TGTTCTTTAG
781 GGATTTCAAG ATTGGAAAAT TTTAGGAGAC GATTGATTTG GAAGTCGGTG AAGTTTCGGT
841 AGTGTTATGT ATTTATTTTT TTTGTCATAA GCGGTAGCGT TATGTATTTG TAAGATCACA
901 TTAAGCGTCT TTCAACTTTG ATTATACGCA TTGCTTCATC TGATATCTAA TCCATATTTT
961 GATCAAAGTG ACATTTGATA AAATAAAATA AAACTAACCT ATTAATATTA TAACTGAGGT
1021 TATTTTTTTA GAAAAAAGAT AGCTAGCTAC ACGAATTATA CGAGAATACA TGGTCACATG
This is an example of two DNA sequences written in FASTA format:
The format is:
TRANSPO RESULTSThe list of transposons found is printed in transpo format and in FASTA format.
The following list of transposons is determined by:
TIR: GGAA Errors: 0 Minimum length: 20 Maximum length: 100
Transposon list in TRANSPO format // LT Left Target XX TS Start position of TIR XX TI Left TIR XX RI Right TIR XX RT Right Target XX BS First position of the transposon XX BE Last position of the transposo XX LE Length of the transposon XX BO Sequence // // LT GTCGA XX TS 152 XX TI GGAA XX RI TTCC XX RT GATCA XX BS 156 XX BE 244 XX LE 90 XX BO AATCTATCGGGTTCGAGGATTCGTCTACCAGGTGATGGAATCCTCGACCAGGACAAAGAATTCGTCGACCAGGGGTGGAATTGTTGTTA // // LT GTGAT XX TS 192 XX TI GGAA XX RI TTCC XX RT GATCA XX BS 196 XX BE 244 XX LE 50 XX BO TCCTCGACCAGGACAAAGAATTCGTCGACCAGGGGTGGAATTGTTGTTA // // LT GGGCG XX TS 454 XX TI GGAA XX RI TTCC XX RT AGAAT XX BS 458 XX BE 519 XX LE 63 XX BO GAGAGAAACTGATGATCAGAGCGATGATGCAGACGTAATTCACCCTGAAATAAGAGGAGTTC // Transposon list in FASTA format >156 AATCTATCGGGTTCGAGGATTCGTCTACCAGGTGATGGAATCCTCGACCAGGACAAAGAATTCGTCGACCAGGGGTGGAATTGTTGTTA >196 TCCTCGACCAGGACAAAGAATTCGTCGACCAGGGGTGGAATTGTTGTTA >458 GAGAGAAACTGATGATCAGAGCGATGATGCAGACGTAATTCACCCTGAAATAAGAGGAGTTC