34 <param name="ex2Fields" type="boolean" checked="false" label="Output sequence in 2 fields (-2, --2_fields)" help="Output each sequence as 2 fields (tag and sequence) on a single line." />
36 <param name="exDir" type="boolean" checked="false" label="Specify sequence direction (-d, --dir)" help="Use the 4th column of each input line to specify the direction of the sequence. Positive is forward, negative is reverse. The input sequence is assumed to be circular." />
40 <param name="exNoStart" type="boolean" checked="false" label="Omit first characters (-s, --nostart)" help="Omit the first 3 characters of each output string." />
42 <param name="exNoStop" type="boolean" checked="false" label="Omit last characters (-t, --nostop)" help="Omit the last 3 characters of each output string." />
44 <param name="exNoWrap" type="boolean" checked="false" label="No wraparound (-w, --nowrap)" help="Use the actual input coordinates without any wraparound that would be needed by a circular genome. Without this option, the output sequence is the shorter of the two ways around the circle. Tick 'Specify sequence direction' to specify direction explicitly." />
58 Read FASTA-format *sequence-file* and extract from it the subsequences specified by *coords*. By default, *coords* is the name of a file containing lines of the form *tag* *start* *stop* [*frame*] ...
59 Coordinates are inclusive counting from 1, e.g. *1 3* represents the 1st 3 characters of the sequence. For each line the corresponding region of *sequence-file* is extracted and output (after reverse-complementing if necessary).
71 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
77 .. |Delcher2007| replace:: Delcher, A. L., Bratke, K. A., Powers, E. C., Salzberg, S. L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. *Bioinformatics* 23(6), 673-679
