]> Reports STOP codons and ORF statistics of a protein (EMBOSS) protein:composition http://bioweb.pasteur.fr/docs/EMBOSS/checktrans.html checktrans &emboss_init; sequence sequence -- stopprotein [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 stopprotein 8 seqsfile perl 1 orfml Minimum ORF Length to report (-orfml) 100 perl (defined $value && $value != $vdef)? " -orfml=$value" : "" 2 1 outfile outfile (-outfile) outfile.out perl " -outfile=$value" 3 outseq outseq (-outseq) outseq.out perl " -outseq=$value" 4 Sequence file to hold output ORF sequences seqsfile perl 1 outseq_sformat Output format for: outseq fasta fasta gcg gcg phylip phylip embl embl swiss swiss ncbi ncbi nbrf nbrf genbank genbank ig ig codata codata strider strider acedb acedb staden staden text text fitch fitch msf msf clustal clustal phylip phylip phylip3 phylip3 asn1 asn1 fasta perl " -osformat=$value" 5 featout featout -- protein (-featout) featout.out perl " -featout=$value" 6 File for output features featout_offormat Feature output format (-offormat) perl ($value)? " -offormat=$value" : "" embl embl gff gff swiss swiss pir pir nbrf nbrf gff 6 addlast Force the sequence to end with an asterisk (-addlast) 1 perl ($value)? "" : " -noaddlast" 7 An asterisk in the protein sequence indicates the position of a STOP codon. Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs. auto perl " -auto -stdout" 8