<?xml version="1.0" encoding="ISO-8859-1" ?>
<!DOCTYPE pise SYSTEM "PARSER/pise.dtd">

<pise>

<head>
    <title>FAStRNA</title>
    <description>Very fast identification of RNA motifs in genomic DNA</description>
    <authors>N. El-Mabrouk</authors>
    <reference>N. El-Mabrouk and F. Lisacek. Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome. J. Mol.Biol., 264:46-55, November 1996.</reference>
</head>


<command>fastrna</command>

<parameters>

<parameter ismandatory="1" iscommand="1" issimple="1" type="Excl">
<name>fastrna</name>
<attributes>

	<format>
		<language>perl</language>
		<code>"$value"</code>
	</format>
	<group>0</group>
	<vlist>
		<value>FAStRNA-CM</value>
		<label>FAStRNA-CM: probabilistic model</label>
		<value>FAStRNA-CLASS</value>
		<label>FAStRNA-CLASS: pattern-matching approach</label>
	</vlist>

</attributes>
</parameter>

<parameter ismandatory="1" issimple="1" type="Sequence">
<name>seq</name>
<attributes>

	<prompt>Sequence File</prompt>
	<format>
		<language>perl</language>
		<code>" $value"</code>
	</format>
	<group>2</group>
	<seqfmt>
		<value>13</value>
	</seqfmt>

</attributes>
</parameter>

<parameter ismandatory="1" type="OutFile">
<name>outfile</name>
<attributes>

	<prompt>Result file</prompt>
	<format>
		<language>perl</language>
		<code>" $value"</code>
	</format>
	<vdef><value>fastrna.res</value></vdef>
	<group>3</group>

</attributes>
</parameter>


</parameters>
</pise>
