http://wiki.christophchamp.com/index.php?action=history&feed=atom&title=BLAST%2Fmatrices BLAST/matrices - Revision history 2026-04-30T12:20:54Z Revision history for this page on the wiki MediaWiki 1.26.2 http://wiki.christophchamp.com/index.php?title=BLAST/matrices&diff=5076&oldid=prev Christoph at 01:07, 16 May 2008 2008-05-16T01:07:10Z <p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;' lang='en'> <td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 01:07, 16 May 2008</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The following are the standard '''[[BLAST]] matrices''' provided by NCBI (last access date: 2008-05-15):</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The following are the standard '''[[BLAST]] matrices''' provided by NCBI (last access date: 2008-05-15):</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> see: [[wikipedia:Substitution matrix|Substitution matrix]]</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==BLOSUM==</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==BLOSUM==</div></td></tr> </table> Christoph http://wiki.christophchamp.com/index.php?title=BLAST/matrices&diff=5075&oldid=prev Christoph at 01:06, 16 May 2008 2008-05-16T01:06:05Z <p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;' lang='en'> <td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 01:06, 16 May 2008</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2" >Line 2:</td> <td colspan="2" class="diff-lineno">Line 2:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==BLOSUM==</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==BLOSUM==</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">'''[[wikipedia:BLOSUM|BLOSUM]]''' ('''BLO'''cks of amino acid '''SU'''bstitution '''M'''atrix)</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM100]</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM100]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM100.50]</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM100.50]</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l34" >Line 34:</td> <td colspan="2" class="diff-lineno">Line 36:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUMN]</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUMN]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUMN.50]</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUMN.50]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==PAM==</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==PAM==</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">'''[[wikipedia:Point Accepted Mutation|PAM]]''' ('''P'''oint '''A'''ccepted '''M'''utation)</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM10]</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM10]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM100]</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM100]</div></td></tr> </table> Christoph http://wiki.christophchamp.com/index.php?title=BLAST/matrices&diff=5069&oldid=prev Christoph at 21:44, 15 May 2008 2008-05-15T21:44:40Z <p></p> <p><b>New page</b></p><div>The following are the standard '''[[BLAST]] matrices''' provided by NCBI (last access date: 2008-05-15):<br /> <br /> ==BLOSUM==<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM100]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM100.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM30]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM30.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM35]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM35.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM40]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM40.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM45]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM45.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM50.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM55]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM55.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM60]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM60.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM62]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM62.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM65]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM65.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM70]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM70.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM75]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM75.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM80]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM80.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM85]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM85.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM90]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM90.50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUMN]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUMN.50]<br /> ==PAM==<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM10]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM100]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM110]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM120]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM120.cdi]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM130]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM140]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM150]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM160]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM160.cdi]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM170]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM180]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM190]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM20]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM200]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM200.cdi]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM210]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM220]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM230]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM240]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM250]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM250.cdi]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM260]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM270]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM280]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM290]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM30]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM300]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM310]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM320]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM330]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM340]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM350]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM360]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM370]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM380]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM390]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM40]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM40.cdi]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM400]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM410]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM420]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM430]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM440]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM450]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM460]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM470]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM480]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM490]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM50]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM500]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM60]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM70]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM80]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM80.cdi]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM90]<br /> ==Other==<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ DAYHOFF]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ GONNET]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ IDENTITY]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ MATCH]<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ NUC.4.2] &amp;mdash; Uses ambiguous nucleotide codes, probabilities rounded to nearest integer<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ NUC.4.4] &amp;mdash; Uses ambiguous nucleotide codes, probabilities rounded to nearest integer<br /> <br /> ==External links==<br /> *[ftp://ftp.ncbi.nlm.nih.gov/blast/ official BLAST download]<br /> <br /> [[Category:Bioinformatics]]</div> Christoph