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<!---#### $Id: mast-databases.html 1339 2006-09-21 19:46:28Z tbailey $#### $Log$## Revision 1.4 2006/03/07 23:30:20 nadya## merge branches v3_5_1 and v3_5_2 back to the trunk#### Revision 1.3.6.1 2006/02/22 20:49:02 nadya## enabling styling with js and css#### Revision 1.3 2005/12/09 06:52:56 tbailey## Added detailed instructions for downloading upstream databases.## Put "K12" after E. coli database name to make clear which strain it is.#### Revision 1.2 2005/08/24 05:28:16 nadya## update links#### Revision 1.1.1.1 2005/07/31 20:13:30 nadya## Importing from meme-3.0.14, and adding configure/make####---><HTML><HEAD><TITLE>Databases available for MAST search</TITLE><script src="template-css.js" type="text/javascript"></script></HEAD><body class="body"><script src="template-header.js" type="text/javascript"></script> <font><H1>MAST -- Motif Alignment and Search Tool</H1><H2><I>Motif search tool</I></H2><HR><H1 ALIGN = center>Sequence databases available for MAST search</H1><HR><H3>The sequence databases that MAST can search are grouped into three categories:<UL> <LI> <A HREF=#assorted>Assorted Databases</A> <BR> Various peptide and nucleotide databases, including those searchable by NCBI BLAST. <LI> <A HREF=#genbank>Genbank Single Organism Databases</A> <BR> Single organism peptide and nucleotide databases from Genbank. <LI> <A HREF=#upstream>Upstream Sequence Databases</A> <BR>Nucleotide sequences located upstream from known genes.</UL></H3><A NAME=assorted></A><HR><H3> Assorted Databases</H3>    <B>Various peptide and nucleotide databases, including those searchable by NCBI BLAST.</B><HR><DL><P><dt><b>alu</b><dd>Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences. It is available by anonymous FTP from ncbi.nih.gov (under the /pub/jmc/alu directory). See "Alu alert" by Claverie and Makalowski, Nature vol. 371, page 752 (1994).<P><DT><B>C. elegans (coding)</B><dd>Wormpep: predicted proteins from the Caenorhabditis elegans genome sequencing project; <A HREF = "http://www.sanger.ac.uk/Projects/C_elegans/wormpep/">http://www.sanger.ac.uk/Projects/C_elegans/wormpep</A>for more information<P><DT><B>C. elegans - coding</B><dd>the DNA sequences from which the Wormpep protein sequences are derived(effectively the cDNA sequence BUT with no UTRs); see<A HREF = "http://www.sanger.ac.uk/Projects/C_elegans/wormpep/">http://www.sanger.ac.uk/Projects/C_elegans/wormpep</A>for more information<P><P><dt><b>Drosophila</b><dd>Drosophila genome proteins and nucleotides provided by Celera and Berkeley <A href="http://www.fruitfly.org">Drosophila Genome Project (BDGP)</A>.<P><DT><B>E. coli</B><dd>Complete E. coli genome proteins and nucleotides from <A HREF=ftp://ftp.ncbi.nih.gov/blast/db/> NCBI BLAST databases</A>.<P><DT><B>epd</B><dd>Eucaryotic Promoter Database found on the web at<a href="http://www.genome.ad.jp/dbget-bin/www_bfind?epd">http://www.genome.ad.jp/dbget-bin/www_bfind?epd</a><P><DT><B>est</B><dd> Non-redundant Database of GenBank+EMBL+DDBJ EST Divisions<P><DT><B>mouse ESTs</B><P><DT><B>human ESTs</B><P><DT><B>other ESTs</B><P><DT><B>genpept</B><DD>GENPEPT peptide database<P><DT><B>gss</B><dd>Genome Survey Sequence, includes single-pass genomic data, exon-trappedsequences, and Alu PCR sequences.<P><dt><b>htgs</b><dd> High Throughput Genomic Sequences<P><dt><b>kabat</b><dd>Kabat's database of peptide and nucleotidesequences of immunological interest.<P><dt><b>mito</b><dd>Database of mitochondrial sequences<P><DT><B>month</B><DD>Peptide: All new or revised GenBank CDS translation+PDB+SwissProt+PIR released in the last 30 days.<DD>Nucleotide: All new or revised GenBank+EMBL+DDBJ+PDB sequences released in the last30 days.<P><DT><B>nr</B><dd>Peptide: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR<DD>Nucleotide: All Non-redundant GenBank+EMBL+DDBJ+PDB sequences (butno EST's or STS's)<P><DT><B>pdb</B><dd>Sequences (peptide and nucleotide) derived from the 3-dimensional structure<A HREF=http://www.rcsb.org/pdb>Protein Data Bank</A>.<P><DT><B>sts</B><dd>Non-redundant Database of GenBank+EMBL+DDBJ STS Divisions<P><DT><B>S. cerevisiae (yeast)</B><dd>Yeast (Saccharomyces cerevisiae) peptide and nucleotide sequences.<P><DT><B>swissprot</B> <dd>The last major release of the SWISS-PROT peptide sequence database (no updates).<P><dt><b>vector</b><dd>Vector subset of GenBank(R), NCBI, in <A HREF=ftp://ftp.ncbi.nih.gov/blast/db/> ftp://ftp.ncbi.nih.gov/blast/db/</A>.</DL><A NAME=genbank></A><HR><H3> Genbank Single Organism Databases</H3>    <B>Single organism peptide (*.faa files) and nucleotide (*.fna files) from <A HREF=ftp://ftp.ncbi.nih.gov/genbank/genomes/README> Genbank.</A></B><HR><P><DT><B>Aeropyrum pernix K1</B><DD>Peptide and nucleotide sequences from Genbank for <I>Aeropyrum pernix K1</I>.<P><DT><B>Archaeoglobus fulgidus</B><DD>Peptide and nucleotide sequences from Genbank for <I>Archaeoglobus fulgidus</I>.<P><DT><B>Aquifex aeolicus</B><DD>Peptide and nucleotide sequences from Genbank for <I>Aquifex aeolicus</I>.<P><DT><B>Aquifex aeolicus ece1</B><DD>Peptide and nucleotide sequences from Genbank for <I>Aquifex aeolicus ece1</I>.<P><DT><B>Borrelia burgdorferi</B><DD>Peptide and nucleotide sequences from Genbank for <I>Borrelia burgdorferi</I>.<P><DT><B>Borrelia burgdorferi 11 plasmids</B><DD>Peptide and nucleotide sequences from Genbank for <I>Borrelia burgdorferi 11 plasmids</I>.<P><DT><B>Bacillus subtilis</B><DD>Peptide and nucleotide sequences from Genbank for <I>Bacillus subtilis</I>.<P><DT><B>Chlamydia trachomatis</B><DD>Peptide and nucleotide sequences from Genbank for <I>Chlamydia trachomatis</I>.<P><DT><B>Chlamydia muridarum</B><DD>Peptide and nucleotide sequences from Genbank for <I>Chlamydia muridarum</I>.<P><DT><B>Chlamydia pneumoniae</B><DD>Peptide and nucleotide sequences from Genbank for <I>Chlamydia pneumoniae</I>.<P><DT><B>Chlamydophila pneumoniae AR39</B><DD>Peptide and nucleotide sequences from Genbank for <I>Chlamydophila pneumoniae AR39</I>.<P><DT><B>Chlamydophila pneumoniae J138</B><DD>Peptide and nucleotide sequences from Genbank for <I>Chlamydophila pneumoniae J138</I>.<P><DT><B>Deinococcus radiodurans R1 chromosome 1</B><DD>Peptide and nucleotide sequences from Genbank for <I>Deinococcus radiodurans R1 chromosome 1</I>.<P><DT><B>Escherichia coli</B><DD>Peptide and nucleotide sequences from Genbank for <I>Escherichia coli</I>.<P><DT><B>Haemophilus influenzae </B><DD>Peptide and nucleotide sequences from Genbank for <I>Haemophilus influenzae </I>.<P><DT><B>Helicobacter pylori 26695</B><DD>Peptide and nucleotide sequences from Genbank for <I>Helicobacter pylori 26695</I>.<P><DT><B>Helicobacter pylori strain J99</B><DD>Peptide and nucleotide sequences from Genbank for <I>Helicobacter pylori strain J99</I>.<P><DT><B>Mycoplasma genitalium</B><DD>Peptide and nucleotide sequences from Genbank for <I>Mycoplasma genitalium</I>.<P><DT><B>Methanococcus jannaschii</B><DD>Peptide and nucleotide sequences from Genbank for <I>Methanococcus jannaschii</I>.<P><DT><B>Methanococcus jannaschii large extrachromosomal element</B><DD>Peptide and nucleotide sequences from Genbank for <I>Methanococcus jannaschii large extrachromosomal element</I>.<P><DT><B>Methanococcus jannaschii small extrachromosomal element</B><DD>Peptide and nucleotide sequences from Genbank for <I>Methanococcus jannaschii small extrachromosomal element</I>.<P><DT><B>Mycoplasma pneumoniae</B><DD>Peptide and nucleotide sequences from Genbank for <I>Mycoplasma pneumoniae</I>.<P><DT><B>Methanobacterium thermoautotrophicum</B><DD>Peptide and nucleotide sequences from Genbank for <I>Methanobacterium thermoautotrophicum</I>.<P><DT><B>Mycobacterium tuberculosis H37Rv</B><DD>Peptide and nucleotide sequences from Genbank for <I>Mycobacterium tuberculosis H37Rv</I>.<P><DT><B>Neisseria meningitidis serogroup B strain MC58</B><DD>Peptide and nucleotide sequences from Genbank for <I>Neisseria meningitidis serogroup B strain MC58</I>.<P><DT><B>Neisseria meningitidis serogroup A strain Z2491</B><DD>Peptide and nucleotide sequences from Genbank for <I>Neisseria meningitidis serogroup A strain Z2491</I>.<P><DT><B>Pyrococcus abyssi</B><DD>Peptide and nucleotide sequences from Genbank for <I>Pyrococcus abyssi</I>.<P><DT><B>Pyrococcus horikoshii</B><DD>Peptide and nucleotide sequences from Genbank for <I>Pyrococcus horikoshii</I>.<P><DT><B>Rhizobium sp. NGR234 complete plasmid sequence</B><DD>Peptide and nucleotide sequences from Genbank for <I>Rhizobium sp. NGR234 complete plasmid sequence</I>.<P><DT><B>Rickettsia prowazekii strain Madrid E</B><DD>Peptide and nucleotide sequences from Genbank for <I>Rickettsia prowazekii strain Madrid E</I>.<P><DT><B>Synechocystis PCC6803</B><DD>Peptide and nucleotide sequences from Genbank for <I>Synechocystis PCC6803</I>.<P><DT><B>Thermotoga maritima</B><DD>Peptide and nucleotide sequences from Genbank for <I>Thermotoga maritima</I>.<P><DT><B>Treponema pallidum</B><DD>Peptide and nucleotide sequences from Genbank for <I>Treponema pallidum</I>.<P><DT><B>Ureaplasma urealyticum</B><DD>Peptide and nucleotide sequences from Genbank for <I>Ureaplasma urealyticum</I>.<P><DT><B>Xylella fastidiosa</B><DD>Peptide and nucleotide sequences from Genbank for <I>Xylella fastidiosa</I>.<A NAME=upstream></A><HR><H3> Upstream Sequence Databases </H3>     <B>Nucleotide sequences located upstream from the coding region of a gene. Each database contains one sequence for each known gene in a particular organism. The origin is at the start codon. The given range of sequence was extracted usingthe <A HREF=http://rsat.scmbb.ulb.ac.be/rsat/>"retrieve sequence"</A> tool (except for Mouse and Human which are from<A HREF="http://arep.med.harvard.edu/labgc/adnan/hsmmupstream/"> George Church Lab</A> at Harvard Medical School.)Negative numbers refer to base pairs upstream of the origin, positive numbers tobase pairs downstream from the origin. </B><HR><P><DT><B> B. subtilis (upstream) </B><DD> Sequence in the range of -500 to +50 relative to the start codon of each gene.<P><DT><B> E. coli K12 (upstream) </B><DD>Sequence in the range of -500 to +50 relative to the start codon of each gene.<P><DT><B> S. cerevisiae (upstream) </B><DD> Sequence in the range of -950 to +50 relative to the start codon of each gene.<P><DT><B> S. cerevisiae (upstream) </B><DD> Sequence in the range of -950 to +50 relative to the start codon of each gene.<P><DT><B> Human (upstream) </B><DD> 5-kb upstream sequences (promoter regions)<P><DT><B> Mouse (upstream) </B><DD> 5-kb upstream sequences (promoter regions)<HR><A HREF="mast.html"><B>Search using MAST</B></A><BR><A href="mast-intro.html"><B>MAST introduction</B></A><BR><A HREF="intro.html"><B>MEME SYSTEM introduction</B></A><script src="template-footer.js" type="text/javascript"></script></BODY></HTML>⌨️ 快捷键说明
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