<BASE HREF="http://meme.sdsc.edu/meme/website/">
<TABLE> 

  <TR>
    <TD>
      <A HREF="mast-databases.html"><B>Sequence database</B></A> to search:
      <SELECT NAME = "database">
        <OPTION VALUE = "Assorted_datbases none none"> -----Assorted Databases-----
	<OPTION VALUE = "alu alu.aa alu.na"> alu
	<OPTION VALUE = "c_elegans c_elegans.aa c_elegans.na"> C. elegans (coding)
	<OPTION VALUE = "c_elegans_cosmids none c_elegans_cosmids.na"> C. elegans (all cosmids)
	<OPTION VALUE = "dicty_gen dicty_gen.aa none"> D. discoideum (Genbank)
	<OPTION VALUE = "dicty_all none dicty_all.na"> D. Discoideum (Other: Sanger+BCM+Jena+Genbank)
	<OPTION VALUE = "drosoph drosoph.aa drosoph.na"> Drosophila 
	<OPTION VALUE = "ecoli ecoli.aa ecoli.na"> E. coli 
	<OPTION VALUE = "epd none epd"> epd
	<OPTION VALUE = "dbest none est"> est
	<OPTION VALUE = "est_human none est_human"> est (human)
	<OPTION VALUE = "est_mouse none est_mouse"> est (mouse)
	<OPTION VALUE = "est_others none est_others"> est (others)
	<OPTION VALUE = "genpept genpept none"> genpept
	<OPTION VALUE = "gss none gss"> gss
	<OPTION VALUE = "htg none htg"> htgs 
	<OPTION VALUE = "kabat kabat.aa kabat.na"> kabat 
	<OPTION VALUE = "mito mito.aa mito.na"> mito
	<OPTION VALUE = "month month.aa month.na"> month
	<OPTION SELECTED VALUE = "nr nr.aa nr.na"> nr
	<OPTION VALUE = "pdb pdb.aa pdb.na"> pdb
	<OPTION VALUE = "dbsts none sts"> sts 
	<OPTION VALUE = "yeast yeast.aa yeast.na"> S. cerevisiae
	<OPTION VALUE = "swissprot swissprot none"> swissprot
	<OPTION VALUE = "vector none vector"> vector
        <OPTION VALUE = "Genbank_single_organism_databases none none"> -----Genbank Single Organism Databases-----
	 <OPTION VALUE = "Aeropyrum_pernix_K1 Aeropyrum_pernix_K1.aa Aeropyrum_pernix_K1.na"> Aeropyrum pernix K1
	 <OPTION VALUE = "Archaeoglobus_fulgidus Archaeoglobus_fulgidus.aa Archaeoglobus_fulgidus.na"> Archaeoglobus fulgidus
	 <OPTION VALUE = "Aquifex_aeolicus Aquifex_aeolicus.aa Aquifex_aeolicus.na"> Aquifex aeolicus
	 <OPTION VALUE = "Aquifex_aeolicus_ece1 Aquifex_aeolicus_ece1.aa Aquifex_aeolicus_ece1.na"> Aquifex aeolicus ece1
	 <OPTION VALUE = "Borrelia_burgdorferi Borrelia_burgdorferi.aa Borrelia_burgdorferi.na"> Borrelia burgdorferi
	 <OPTION VALUE = "Borrelia_burgdorferi_11_plasmids Borrelia_burgdorferi_11_plasmids.aa Borrelia_burgdorferi_11_plasmids.na"> Borrelia burgdorferi 11 plasmids
	 <OPTION VALUE = "Bacillus_subtilis Bacillus_subtilis.aa Bacillus_subtilis.na"> Bacillus subtilis
	 <OPTION VALUE = "Chlamydia_trachomatis Chlamydia_trachomatis.aa Chlamydia_trachomatis.na"> Chlamydia trachomatis
	 <OPTION VALUE = "Chlamydia_muridarum Chlamydia_muridarum.aa Chlamydia_muridarum.na"> Chlamydia muridarum
	 <OPTION VALUE = "Chlamydia_pneumoniae Chlamydia_pneumoniae.aa Chlamydia_pneumoniae.na"> Chlamydia pneumoniae
	 <OPTION VALUE = "Chlamydophila_pneumoniae_AR39 Chlamydophila_pneumoniae_AR39.aa Chlamydophila_pneumoniae_AR39.na"> Chlamydophila pneumoniae AR39
	 <OPTION VALUE = "Chlamydophila_pneumoniae_J138 Chlamydophila_pneumoniae_J138.aa Chlamydophila_pneumoniae_J138.na"> Chlamydophila pneumoniae J138
	 <OPTION VALUE = "Deinococcus_radiodurans_R1_chromosome_1 Deinococcus_radiodurans_R1_chromosome_1.aa Deinococcus_radiodurans_R1_chromosome_1.na"> Deinococcus radiodurans R1 chromosome 1
	 <OPTION VALUE = "Eschericia_coli Eschericia_coli.aa Eschericia_coli.na"> Eschericia coli
	 <OPTION VALUE = "Haemophilus_influenzae_Rd Haemophilus_influenzae_Rd.aa Haemophilus_influenzae_Rd.na"> Haemophilus influenzae Rd
	 <OPTION VALUE = "Helicobacter_pylori_26695 Helicobacter_pylori_26695.aa Helicobacter_pylori_26695.na"> Helicobacter pylori 26695
	 <OPTION VALUE = "Helicobacter_pylori_strain_J99 Helicobacter_pylori_strain_J99.aa Helicobacter_pylori_strain_J99.na"> Helicobacter pylori strain J99
	 <OPTION VALUE = "Mycoplasma_genitalium Mycoplasma_genitalium.aa Mycoplasma_genitalium.na"> Mycoplasma genitalium
	 <OPTION VALUE = "Methanococcus_jannaschii Methanococcus_jannaschii.aa Methanococcus_jannaschii.na"> Methanococcus jannaschii
	 <OPTION VALUE = "Methanococcus_jannaschii_large_extrachromosomal_element Methanococcus_jannaschii_large_extrachromosomal_element.aa Methanococcus_jannaschii_large_extrachromosomal_element.na"> Methanococcus jannaschii large extrachromosomal element
	 <OPTION VALUE = "Methanococcus_jannaschii_small_extrachromosomal_element Methanococcus_jannaschii_small_extrachromosomal_element.aa Methanococcus_jannaschii_small_extrachromosomal_element.na"> Methanococcus jannaschii small extrachromosomal element
	 <OPTION VALUE = "Mycoplasma_pneumoniae Mycoplasma_pneumoniae.aa Mycoplasma_pneumoniae.na"> Mycoplasma pneumoniae
	 <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 = "Upstream_sequence_databases 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 (upstream)
	  <OPTION VALUE = "S.cerevisiae_upstream none yeast_-950_50.na"> S. cerevisiae (upstream)
      </SELECT>

   <TD>
     <INPUT TYPE = "SUBMIT" value="Start search"> &nbsp &nbsp &nbsp
     <INPUT TYPE = "RESET" value="Clear Input">

  <TR>
    <TH COLSPAN=2> <HR> OPTIONS <HR>

  <TR>
    <TD>
      <INPUT 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

    <TD>
      <A HREF="mast-input.html#description"><B>Description</B></A>
      of your motifs:
      <INPUT TYPE = "TEXT" SIZE = 40 NAME = "subject">

  <TR>
    <TD>
      <INPUT 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>
      <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>

  <TR>
    <TD>
      <INPUT TYPE = "CHECKBOX" NAME = "text" value="-text"> 
      <A HREF="mast-input.html#text"><B>Text</B></A> output format

    <TD>
      <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>
  <TR>
    <TD>
    <TD>
      <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
      </SELECT>

  <TR>
    <TH COLSPAN=2> <HR> DNA-ONLY OPTIONS <HR>

  <TR>
    <TD>
      <INPUT TYPE = "CHECKBOX" NAME = "dna" value="-dna"> 
      <A HREF="mast-input.html#dna"><B>Search nucleotide</B></A> database
      with protein motifs

    <TD>
      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> 

    <TR>
      <TD COLSPAN = 2> <HR>

    <TR>
      <TD>
        <INPUT TYPE = "SUBMIT" value="Start search"> &nbsp &nbsp &nbsp
        <INPUT TYPE = "RESET" value="Clear Input">
</TABLE>

</TABLE>
<HR>
Click here for 
<A HREF="mast-intro.html"><B>more information</B></A> 
on <B>MAST</B>.

<BR>
Return to 
<A HREF="intro.html"><B>MEME SYSTEM introduction</B></A>.

<P>
<I>Please send comments and questions to:
<A HREF="mailto:tbailey@sdsc.edu">tbailey@sdsc.edu</A>.</B>

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