]> Trimming and validation of DNA sequences (TIGR) edit http://www.tigr.org/tdb/tgi/software/ seqclean &blast_init; seqclean perl ($vecdbs) ? "formatdb -i $vecdbs -n $vecdbs -oT -pF && seqclean" : "seqclean" 1 sequence DNA sequence(s) to be cleaned perl " $value" dna 3 8 report report file (-r) report.txt perl " -r $value" 3 cleaned_seq output the \"cleaned\" sequences to file (-o) cleaned.txt perl " -o $value" 4 univec Contaminant database UniVec UniVec UniVec vector database None perl (defined $value)? " -v $ENV{BLASTDB}/$value":"" 5 Available contaminant databases vecdbs Custom contaminant sequences perl (defined $value && $value ) ? ((defined $univec && $univec) ? ",$value" : " -v $value") : "" dna 6 8 Custom contaminant sequence(s). When it appears that after cleaning your sequences is still contaminated, provide your contaminating (vector) sequence(s) here. length Minimal length 100 perl (defined $value && $value != $vdef)? " -l $value":"" During cleaning, consider invalid the sequences shorter than the entered length (default 100) A sequence that gets shorter than this value by end trimming (undetermined bases, polyA or vector clipping) gets trashed no_end_trimming Disable trimming of ends rich in Ns (undetermined bases) 0 perl $value ? " -N" : "" 6 Ns at the end are trimmed by default. You can disable this behaviour by setting this option. no_polyA_trimming Disable trimming of polyA/T tails 0 perl $value ? " -A" : "" 7 PolyA stretches at the end are trimmed by default. You can disable this behaviour by setting this option. no_dust Disable low-complexity screening (dust) 0 perl $value ? " -L" : "" 8 The sequence is screened for low-complexity regions by default. You can disable this behaviour by setting this option.