Hi, I am a new user of emboss. I am trying to find repeat sequences in a nucleotide sequence file that have many sequences.
Can anybody tell me how to use einverted and etandem to analyze all the sequences in a fasta file? Many Thanks. Sincerely Zheng, yun Dept of Computer Science and Engineering Washington Univ in St Louis Campus Box 1045 1 Brookings Drive Jolley Hall 505 St Louis, MO 63130 Details: I install a version on the linux platform. And the command is like follows, where the default value is used. >einverted -sequence test.fasta -outfile test.outfile -outseq >test-i.fasta Finds DNA inverted repeats Gap penalty [12]: Minimum score threshold [50]: Match score [3]: Mismatch score [-4]: But the output file seems always to be empty. When I try etandom >etandem -sequence test.fasta -outfile test-t.out -origfile test.etandem Looks for tandem repeats in a nucleotide sequence Minimum repeat size [10]: Maximum repeat size [10]: 18 However, it seems that only the first sequence is analyzed by the einverted and etandom. The test-t.out file is as follows. ######################################## # Program: etandem # Rundate: Sat Oct 28 2006 17:24:30 # Commandline: etandem # -sequence test.fasta # -outfile test-t.out # -origfile test.etandem # -maxrepeat 18 # Report_format: table # Report_file: test-t.out ######################################## #======================================= # # Sequence: D9X6RJV01EER0J from: 1 to: 55 # HitCount: 0 # # Threshold: 20 # Minrepeat: 10 # Maxrepeat: 18 # Mismatch: No # Uniform: No # #======================================= Start End Score Size Count Identity Consensus #--------------------------------------- #--------------------------------------- Many thanks. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
