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CH391L/BLOSUM - Revision history
2024-03-29T07:57:20Z
Revision history for this page on the wiki
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http://www.marcottelab.org/index.php?title=CH391L/BLOSUM&diff=727&oldid=prev
Taejoon: /* Comments */
2011-02-10T02:44:05Z
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<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 02:44, 10 February 2011</td>
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<tr><td class='diff-marker'> </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'> </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'> </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>== Comments ==</div></td><td class='diff-marker'> </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>== Comments ==</div></td></tr>
<tr><td colspan="2"> </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;">Two 'not-easy' method used to read BLOSUM table in PERL. </ins></div></td></tr>
<tr><td colspan="2"> </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"> </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;"> my @aa1_list = split(/\s+/,$aa1_line);</ins></div></td></tr>
<tr><td colspan="2"> </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;">* This splits the line with whitespace (space, tab, etc.). The pattern in '//' sign is called regular expression (I mentioned this in my lecture), and it recognize a pattern in the string. For example, '\s+' means 'one or more(+) whitespace(\s)'. You can find more information about PERL regular expression at http://perldoc.perl.org/perlretut.html .</ins></div></td></tr>
<tr><td colspan="2"> </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"> </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;"> $score_map{$tmp[0]}->{$aa1_list[$i]} = $tmp[$i];</ins></div></td></tr>
<tr><td colspan="2"> </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;">* This is called 'hash of hashes'. The reason why I use this data structure is (1) I cannot initialize two dimensional array in PERL (means it is little bit complex to handle this in array form), and (2) all I need is to access the value with two amino acids. $tmp[0] (row) and $aa_list[$i] (column) are two amino acids, and $tmp[$i] is BLOSUM50 score for their substitution. As you see later in the code, you can call this score by $score_map{'A'}->{'S'}. See [http://www.cs.mcgill.ca/~abatko/computers/programming/perl/howto/hash/#create_a_hash_of_hashes__via_references here] for more about 'hash of hashes'.</ins></div></td></tr>
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Taejoon
http://www.marcottelab.org/index.php?title=CH391L/BLOSUM&diff=726&oldid=prev
Taejoon: Created page with "== Source Code == * http://www.marcottelab.org/users/CH391L/FromTA/BLOSUM.pl.txt * You also need BLOSUM50.txt file to run this script: http://www.marcottelab.org/users/CH391L/Fro..."
2011-02-09T21:21:35Z
<p>Created page with "== Source Code == * http://www.marcottelab.org/users/CH391L/FromTA/BLOSUM.pl.txt * You also need BLOSUM50.txt file to run this script: http://www.marcottelab.org/users/CH391L/Fro..."</p>
<p><b>New page</b></p><div>== Source Code ==<br />
* http://www.marcottelab.org/users/CH391L/FromTA/BLOSUM.pl.txt<br />
* You also need BLOSUM50.txt file to run this script: http://www.marcottelab.org/users/CH391L/FromTA/BLOSUM50.txt<br />
<br />
== How it works ==<br />
http://www.marcottelab.org/users/CH391L/FromTA/BLOSUM_output.jpg<br />
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== Comments ==<br />
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[[Category:CH391L]]</div>
Taejoon