mast.in

EM算法的改进

                  <OPTION VALUE = "Methanobacterium_thermoautotrophicum Methanobacterium_thermoautotrophicum.aa Methanobacterium_thermoautotrophicum.na"> Methanobacterium thermoautotrophicum
                  <OPTION VALUE = "Mycobacterium_tuberculosis_H37Rv Mycobacterium_tuberculosis_H37Rv.aa Mycobacterium_tuberculosis_H37Rv.na"> Mycobacterium tuberculosis H37Rv
                  <OPTION VALUE = "Neisseria_meningitidis_serogroup_B_strain_MC58 Neisseria_meningitidis_serogroup_B_strain_MC58.aa Neisseria_meningitidis_serogroup_B_strain_MC58.na"> Neisseria meningitidis serogroup B strain MC58
                  <OPTION VALUE = "Neisseria_meningitidis_serogroup_A_strain_Z2491 Neisseria_meningitidis_serogroup_A_strain_Z2491.aa Neisseria_meningitidis_serogroup_A_strain_Z2491.na"> Neisseria meningitidis serogroup A strain Z2491
                  <OPTION VALUE = "Pyrococcus_abyssi Pyrococcus_abyssi.aa Pyrococcus_abyssi.na"> Pyrococcus abyssi
                  <OPTION VALUE = "Pyrococcus_horikoshii Pyrococcus_horikoshii.aa Pyrococcus_horikoshii.na"> Pyrococcus horikoshii
                  <OPTION VALUE = "Rhizobium_sp._NGR234_complete_plasmid_sequence Rhizobium_sp._NGR234_complete_plasmid_sequence.aa Rhizobium_sp._NGR234_complete_plasmid_sequence.na"> Rhizobium sp. NGR234 complete plasmid sequence
                  <OPTION VALUE = "Rickettsia_prowazekii_strain_Madrid_E Rickettsia_prowazekii_strain_Madrid_E.aa Rickettsia_prowazekii_strain_Madrid_E.na"> Rickettsia prowazekii strain Madrid E
                  <OPTION VALUE = "Synechocystis_PCC6803 Synechocystis_PCC6803.aa Synechocystis_PCC6803.na"> Synechocystis PCC6803
                  <OPTION VALUE = "Thermotoga_maritima Thermotoga_maritima.aa Thermotoga_maritima.na"> Thermotoga maritima
                  <OPTION VALUE = "Treponema_pallidum Treponema_pallidum.aa Treponema_pallidum.na"> Treponema pallidum
                  <OPTION VALUE = "Ureaplasma_urealyticum Ureaplasma_urealyticum.aa Ureaplasma_urealyticum.na"> Ureaplasma urealyticum
                  <OPTION VALUE = "Xylella_fastidiosa Xylella_fastidiosa.aa Xylella_fastidiosa.na"> Xylella fastidiosa
                  <OPTION VALUE = "none none none"> -----Upstream Sequence Databases-----
                  <OPTION VALUE = "B.subtilis_upstream none bsubtilis_-500_50.na"> B. subtilis (upstream)
                  <OPTION VALUE = "E.coli_upstream none ecoli_-500_50.na"> E. coli K12 (upstream)
                  <OPTION VALUE = "S.cerevisiae_upstream none yeast_-950_50.na"> S. cerevisiae (upstream)
                  <OPTION VALUE = "human_upstream none hs.upstream.na"> Human (upstream)
                  <OPTION VALUE = "mouse_upstream none mouse.upstream.na"> Mouse (upstream)
                </SELECT>
		<br>
		<b>or</b>
		<br>
              Your <A HREF="mast-input.html#FASTA"><B>FASTA</B></A> sequence file (1,000,000 sequence characters maximum):<BR>
                <A HREF="examples/sample-kabat.seq">Sample</A> DNA sequence, right click and "save target as" to download. <BR>
                <!-- Note: change $MAX_UPLOAD_SIZE in mast.cgi if you change this. -->
                <B>
                <INPUT class="maininput" NAME="upload_db" TYPE="file">
                </B>
            </UL></td>
        </tr>
      </table>
      <nobr>
      <center>
        <label class="mainheadingmedium">Optional</label>
      </center>
      <table>
        <tr>
          <td valign="top">
	    <font>	
	    <A HREF="mast-input.html#description"><B>Description</B></A> of your motifs:
            <INPUT class="maininput" TYPE = "TEXT" SIZE = 40 NAME = "subject">
            <br>
            <A HREF="mast-input.html#rank"><B>Rank</B></A> of the first match returned: <B>
            <SELECT NAME = "rank">
              <OPTION SELECTED> 1
              <OPTION> 501
              <OPTION> 1001
              <OPTION> 1501
              <OPTION> 2001
              <OPTION> 2501
              <OPTION> 3001
              <OPTION> 3501
              <OPTION> 4001
              <OPTION> 4501
              <OPTION> 5001
              <OPTION> 5501
              <OPTION> 6001
              <OPTION> 6501
              <OPTION> 7001
              <OPTION> 7501
              <OPTION> 8001
              <OPTION> 8501
              <OPTION> 9001
              <OPTION> 9501
              <OPTION> 10001
            </SELECT>
            </B> <br>
            <A HREF="mast-input.html#ev"><B>Display sequences with <I>E</I>-value below:</B></A>
            <SELECT NAME = "ev">
              <OPTION VALUE = "-ev 0.01"> 0.01
              <OPTION VALUE = "-ev 0.1"> 0.1
              <OPTION VALUE = "-ev 1"> 1
              <OPTION SELECTED VALUE = "-ev 10"> 10
              <OPTION VALUE = "-ev 20"> 20
              <OPTION VALUE = "-ev 50"> 50
              <OPTION VALUE = "-ev 100"> 100
              <OPTION VALUE = "-ev 200"> 200
              <OPTION VALUE = "-ev 500"> 500
              <OPTION VALUE = "-ev 1000"> 1000
            </SELECT>
            <br>
            <A HREF="mast-input.html#mev"><B>Ignore motifs if <I>E</I>-value above:</B></A>
            <SELECT NAME = "mev">
              <OPTION SELECTED VALUE = ""> use all motifs
              <OPTION VALUE = "-mev 100"> 100
              <OPTION VALUE = "-mev 50"> 50
              <OPTION VALUE = "-mev 20"> 20
              <OPTION VALUE = "-mev 10"> 10
              <OPTION VALUE = "-mev 5"> 5
              <OPTION VALUE = "-mev 2"> 2
              <OPTION VALUE = "-mev 1"> 1
              <OPTION VALUE = "-mev .5"> .5
              <OPTION VALUE = "-mev .2"> .2
              <OPTION VALUE = "-mev .1"> .1
              <OPTION VALUE = "-mev .05"> .05
              <OPTION VALUE = "-mev .02"> .02
              <OPTION VALUE = "-mev .01"> .01
              <OPTION VALUE = "-mev .005"> .005
              <OPTION VALUE = "-mev .002"> .002
              <OPTION VALUE = "-mev .001"> .001
              <OPTION VALUE = "-mev 1e-5"> 1e-5
              <OPTION VALUE = "-mev 1e-10"> 1e-10
              <OPTION VALUE = "-mev 1e-50"> 1e-50
              <OPTION VALUE = "-mev 1e-100"> 1e-100
            </SELECT>
            <br>
            <INPUT class="mainbutton" TYPE = "CHECKBOX" NAME = "use_seq_comp" value="-comp">
            <A HREF="mast-input.html#use_seq_comp"><B> Use individual sequence composition</B></A> <BR>
            in <I>E</I>- and <I>p</I>-value calculation </td>
          <td valign="top"><INPUT class="mainbutton" TYPE = "CHECKBOX" NAME = "use_seq_p" value="-seqp -mt 0.01">
            <A HREF="mast-input.html#use_seq_p"><B>Scale motif display threshold</B> </A> by sequence length; <B>recommended</B> for <B>nucleotide</B> searches <br>
            <INPUT class="mainbutton" TYPE = "CHECKBOX" NAME = "text" value="-text">
            <A HREF="mast-input.html#text"><B>Text</B></A> output format <br>
            <center>
              <B>DNA-ONLY OPTIONS</B>
            </center>
            <INPUT class="mainbutton" TYPE = "CHECKBOX" NAME = "dna" value="-dna">
            <A HREF="mast-input.html#dna"><B>Search nucleotide</B></A> database with protein motifs
	    <br>	
            Treatment of <A HREF="mast-input.html#strands"><B>reverse complement</B></A> strands:
              <SELECT NAME = "strands">
                <OPTION SELECTED VALUE = ",combine"> combine with given strand
                <OPTION VALUE = "-sep,separate"> treat as separate sequence
                <OPTION VALUE = "-norc,none"> none
              </SELECT>
            </font></td>
      </table>
      <br>
      <center>
        <INPUT class="maininput" TYPE = "SUBMIT" value="Start search" onClick="return check(this.form)">
&nbsp &nbsp &nbsp
        <INPUT class="maininput" TYPE = "RESET" value="Clear Input">
        <br>
        <P>Please send comments and questions to: <A HREF="mailto:[e-mail]">[e-mail]</A>.</B>
      </center>
      </fieldset>
</FORM>
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<td><a href="release_notes.html">Release Notes</a></td>
<td><a href="papers.html">Papers</a></td>
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