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

<pise>

<head>
    <title>ProDom</title>
    <description>PRODOM Protein Domain Database</description>
    <authors>Sonnhammer &amp; Kahn</authors>
    <reference>Sonnhammer ELL and Kahn D. The modular arrangement of proteins as Inferred from Analysis of Homology. Protein Science 3:482-492 (1994).</reference>
</head>


<command>prodom</command>

<parameters>

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

	<prompt>Prodom program</prompt>
	<format>
		<language>perl</language>
		<code>"$value"</code>
	</format>
	<vdef><value>askdom</value></vdef>
	<group>1</group>
	<vlist>
		<value>askdom</value>
		<label>askdom: Query ProDom for the domain organization of a known protein</label>
		<value>fetchmul</value>
		<label>fetchmul: Fetch a Domain Family</label>
		<value>fetchcon</value>
		<label>fetchcon: Fetch a Domain Family Consensus Sequence</label>
	</vlist>
	<comment>
		<value>You can also perform a Blast search on the prodom database (see various Blast forms on this server).</value>
	</comment>

</attributes>
</parameter>

<parameter ismandatory="1" issimple="1" type="String">
<name>entry_name</name>
<attributes>

	<prompt>Entry name of a known protein</prompt>
	<format>
		<language>perl</language>
		<code>" $value"</code>
	</format>
	<group>2</group>
	<comment>
		<value>Query ProDom for the domain organization of a known protein, given its entry name</value>
	</comment>
<precond>
	<language>perl</language>
	<code>$prodom eq "askdom"</code>
</precond>

</attributes>
</parameter>

<parameter ismandatory="1" type="String">
<name>family_number</name>
<attributes>

	<prompt>(or) Family number</prompt>
	<format>
		<language>perl</language>
		<code>" $value"</code>
	</format>
	<group>2</group>
	<comment>
		<value>Family number which description or consensus sequence you want by fetchmul or fetchcon.</value>
		<value>Family numbers can be given by a first query to askdom.</value>
	</comment>
<precond>
	<language>perl</language>
	<code>$prodom ne "askdom"</code>
</precond>

</attributes>
</parameter>


</parameters>
</pise>
