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glossary.html

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   <a href="./intro.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./blast.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">BLAST</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./summary.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
@@ -814,7 +820,7 @@ <h2 class="anchored" data-anchor-id="subject-sequence">Subject Sequence</h2>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
       <a href="./summary.html" class="pagination-link" aria-label="Summary">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span>
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Summary</span></span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">

index.html

@@ -126,11 +126,17 @@
   <a href="./intro.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./blast.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">BLAST</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./summary.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">

intro.html

@@ -51,7 +51,7 @@
 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
-<link href="./summary.html" rel="next">
+<link href="./blast.html" rel="next">
 <link href="./index.html" rel="prev">
 <link href="./icon_32.png" rel="icon" type="image/png">
 <script src="site_libs/quarto-html/quarto.js"></script>
@@ -147,11 +147,17 @@
   <a href="./intro.html" class="sidebar-item-text sidebar-link active">
  <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./blast.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">BLAST</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./summary.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
@@ -815,8 +821,8 @@ <h3 data-number="1.4.5" class="anchored" data-anchor-id="interpro"><span class="
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./summary.html" class="pagination-link" aria-label="Summary">
-        <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span> <i class="bi bi-arrow-right-short"></i>
+      <a href="./blast.html" class="pagination-link" aria-label="BLAST">
+        <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">BLAST</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>

references.html

@@ -145,11 +145,17 @@
   <a href="./intro.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./blast.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">BLAST</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./summary.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
@@ -195,6 +201,23 @@ <h1 class="title">References</h1>
 
 
 <div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" role="list">
+<div id="ref-Altschul1990-ar" class="csl-entry" role="listitem">
+Altschul, S F, W Gish, W Miller, E W Myers, and D J Lipman. 1990.
+<span>“Basic Local Alignment Search Tool.”</span> <em>J. Mol. Biol.</em>
+215 (3): 403–10.
+</div>
+<div id="ref-Altschul1997-vt" class="csl-entry" role="listitem">
+Altschul, S F, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, and
+D J Lipman. 1997. <span>“Gapped <span>BLAST</span> and
+<span>PSI-BLAST</span>: A New Generation of Protein Database Search
+Programs.”</span> <em>Nucleic Acids Res.</em> 25 (17): 3389–3402.
+</div>
+<div id="ref-Camacho2009-za" class="csl-entry" role="listitem">
+Camacho, Christiam, George Coulouris, Vahram Avagyan, Ning Ma, Jason
+Papadopoulos, Kevin Bealer, and Thomas L Madden. 2009.
+<span>“<span>BLAST+</span>: Architecture and Applications.”</span>
+<em>BMC Bioinformatics</em> 10 (1): 421.
+</div>
 <div id="ref-Olivella2013-rm" class="csl-entry" role="listitem">
 Olivella, Mireia, Angel Gonzalez, Leonardo Pardo, and Xavier Deupi.
 2013. <span>“Relation Between Sequence and Structure in Membrane
@@ -206,6 +229,17 @@ <h1 class="title">References</h1>
 Predict Protein Function.”</span> <em>PLoS Comput. Biol.</em> 4 (10):
 e1000160.
 </div>
+<div id="ref-Steinegger2017-sy" class="csl-entry" role="listitem">
+Steinegger, Martin, and Johannes Söding. 2017.
+<span>“<span>MMseqs2</span> Enables Sensitive Protein Sequence Searching
+for the Analysis of Massive Data Sets.”</span> <em>Nat. Biotechnol.</em>
+35 (11): 1026–28.
+</div>
+<div id="ref-Zhang2000-wn" class="csl-entry" role="listitem">
+Zhang, Z, S Schwartz, L Wagner, and W Miller. 2000. <span>“A Greedy
+Algorithm for Aligning <span>DNA</span> Sequences.”</span> <em>J.
+Comput. Biol.</em> 7 (1-2): 203–14.
+</div>
 <div id="ref-Zhou2019-ny" class="csl-entry" role="listitem">
 Zhou, Naihui, Yuxiang Jiang, Timothy R Bergquist, Alexandra J Lee,
 Balint Z Kacsoh, Alex W Crocker, Kimberley A Lewis, et al. 2019.

search.json

@@ -89,14 +89,34 @@
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+    "title": "2  BLAST",
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+    "text": "2.1 Performing a BLAST search\nThis section descbribes a general BLAST query using the NCBI BLAST server. It is intended as a reference guide for you to return to as you get used to querying BLAST through this interface.",
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+    "href": "blast.html#performing-a-blast-search",
+    "title": "2  BLAST",
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+    "text": "Caution\n\n\n\nThere are implementations of BLAST or other sequence search methods at many other databases, and they may present a different interface and choice of options, or even a totally different search method. For example, the RCSB-PDB protein structure database offers a sequence search page which uses the mmseqs2 search algorithm (Steinegger and Söding (2017)).\n\n\n\n2.1.1 Navigate to the NCBI BLAST webserver\nOpen a web browser and navigate to the NCBI BLAST webserver. You should see a landing page that resembles Figure 2.1.\n\n\n\n\n\n\nFigure 2.1: The landing page of the NCBI BLAST webserver.\n\n\n\n\n\n\n\n\n\nYou can use an NCBI account to save searches\n\n\n\n\n\nNote that there is a Log in button at the top right of the landing page. If you have a suitable account with NCBI/NIH, NCBI maintains a record of your searches and history so you can store your searches and retrieve them later.\n\nSign up for a free NCBI account\n\n\n\n\n\n\n2.1.2 Select the BLAST tool you want to use\nThe BLAST suite provides search tools for finding matches to a query in a database. The query can be either a nucleotide or a protein sequence, and the database being searched can contain either protein sequences or nucleotide sequences. BLAST provides four different programs to carry out these combinations of search.\n\n\n\nTable 2.1: The four main BLAST programs, and the combination of query/database sequence type they are used for\n\n\n\n\n\nQuery type\nnucleotideDB\nproteinDB\n\n\n\n\nnucleotide\nblastn\nblastx\n\n\nprotein\ntblastn\nblastp\n\n\n\n\n\n\n\n\n\n\n\n\nSpecialised BLAST tools\n\n\n\n\n\nThe NCBI BLAST webserver provides specialised search options with specific combinations of parameters and databases pre-selected to support particular kinds of search (Figure 2.2).\n\n\n\n\n\n\nFigure 2.2: Specialised BLAST search options are available at the NCBI BLAST webserver\n\n\n\n\n\n\nSelect Nucleotide BLAST from the NCBI landing page, to get to the blastn search page (Figure 2.3).\n\n\n\n\n\n\nFigure 2.3: The NCBI blastn webservice search page\n\n\n\n\n\n2.1.3 Enter the query sequence\nCopy the DNA sequence below, and paste it into the box marked  Enter accession number(s), gi(s), or FASTA sequence(s) at the NCBI search page (Figure 2.4).\nATGCGTCGAGGGCGTCTGCTGGAGATCGCCCTGGGATTTACCGTGCT\nTTTAGCGTCCTACACGAGCCATGGGGCGGACGCCAATTTGGAGGC\nTGGGAACGTGAAGGAAACCAGAGCCAGTCGGGCC\n\n\n\n\n\n\nFigure 2.4: The NCBI blastn search page with a query sequence pasted into the query sequence field.\n\n\n\n\n\n2.1.4 Set appropriate parameter choices\n\n\n\n\n\n\nCaution\n\n\n\nIf you make no more changes to the parameter settings for your search, the default options will be used. Your query will be made against the nr/nt complete nucleotide collection, a very large database. Due to the size of the database, the search may take a relatively long time.\n\n\n\n\n\n\n\n\nImproving your searches by changing parameters\n\n\n\n\n\nYou can make your BLAST searches quicker, and more relevant to your biological question, if you can use information about your sequence and the type of organism you want to search.\nNCBI BLAST offers a number of smaller specialised databases with particular sequence types (e.g. RNA databases, sequences of protein structures, etc.) (Figure 2.5).\n\n\n\n\n\n\nFigure 2.5: A list of specialised sequence databases offered by the NCBI BLAST webserver\n\n\n\nYou can also narrow down the search by specifying an organism, or other taxonomic rank, using the Organism field (Figure 2.6).\n\n\n\n\n\n\nFigure 2.6: Taxonomic options offered by the NCBI BLAST search organism field, for “Pseudomonas”\n\n\n\n\n\n\nRestrict the sequences being searched by typing “Homo sapiens” in the Organism field and selecting the appropriate option from the drop-down list (Figure 2.7).\n\n\n\n\n\n\nFigure 2.7: Taxonomic options offered by the NCBI BLAST search organism field, for “Homo sapiens”\n\n\n\n\n\n2.1.5 Run the BLAST search\nClick on the BLAST button (Figure 2.8).\n\n\n\n\n\n\nFigure 2.8: The NCBI BLAST webserver BLAST button. Click this to start the search.\n\n\n\n\n\n2.1.6 Wait for the search to complete\nWhile the search runs, you will see a holding page that updates you with progress (Figure 2.9)\n\n\n\n\n\n\nFigure 2.9: An NCBI BLAST webserver progress page.\n\n\n\nWhen the search is complete, you will see the blastn results page (Figure 2.10).\n\n\n\n\n\n\nFigure 2.10: An NCBI BLAST results page, for a blastn query.\n\n\n\n\n\n\n\nAltschul, S F, W Gish, W Miller, E W Myers, and D J Lipman. 1990. “Basic Local Alignment Search Tool.” J. Mol. Biol. 215 (3): 403–10.\n\n\nAltschul, S F, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, and D J Lipman. 1997. “Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs.” Nucleic Acids Res. 25 (17): 3389–3402.\n\n\nCamacho, Christiam, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, and Thomas L Madden. 2009. “BLAST+: Architecture and Applications.” BMC Bioinformatics 10 (1): 421.\n\n\nSteinegger, Martin, and Johannes Söding. 2017. “MMseqs2 Enables Sensitive Protein Sequence Searching for the Analysis of Massive Data Sets.” Nat. Biotechnol. 35 (11): 1026–28.\n\n\nZhang, Z, S Schwartz, L Wagner, and W Miller. 2000. “A Greedy Algorithm for Aligning DNA Sequences.” J. Comput. Biol. 7 (1-2): 203–14.",
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     "text": "In summary, this book has no content whatsoever.\n\n1 + 1\n\n[1] 2",
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-    "text": "Olivella, Mireia, Angel Gonzalez, Leonardo Pardo, and Xavier Deupi.\n2013. “Relation Between Sequence and Structure in Membrane\nProteins.” Bioinformatics 29 (13): 1589–92.\n\n\nPunta, Marco, and Yanay Ofran. 2008. “The Rough Guide to in Silico\nFunction Prediction, or How to Use Sequence and Structure Information to\nPredict Protein Function.” PLoS Comput. Biol. 4 (10):\ne1000160.\n\n\nZhou, Naihui, Yuxiang Jiang, Timothy R Bergquist, Alexandra J Lee,\nBalint Z Kacsoh, Alex W Crocker, Kimberley A Lewis, et al. 2019.\n“The CAFA Challenge Reports Improved Protein Function\nPrediction and New Functional Annotations for Hundreds of Genes Through\nExperimental Screens.” Genome Biol. 20 (1): 244.",
+    "text": "Altschul, S F, W Gish, W Miller, E W Myers, and D J Lipman. 1990.\n“Basic Local Alignment Search Tool.” J. Mol. Biol.\n215 (3): 403–10.\n\n\nAltschul, S F, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, and\nD J Lipman. 1997. “Gapped BLAST and\nPSI-BLAST: A New Generation of Protein Database Search\nPrograms.” Nucleic Acids Res. 25 (17): 3389–3402.\n\n\nCamacho, Christiam, George Coulouris, Vahram Avagyan, Ning Ma, Jason\nPapadopoulos, Kevin Bealer, and Thomas L Madden. 2009.\n“BLAST+: Architecture and Applications.”\nBMC Bioinformatics 10 (1): 421.\n\n\nOlivella, Mireia, Angel Gonzalez, Leonardo Pardo, and Xavier Deupi.\n2013. “Relation Between Sequence and Structure in Membrane\nProteins.” Bioinformatics 29 (13): 1589–92.\n\n\nPunta, Marco, and Yanay Ofran. 2008. “The Rough Guide to in Silico\nFunction Prediction, or How to Use Sequence and Structure Information to\nPredict Protein Function.” PLoS Comput. Biol. 4 (10):\ne1000160.\n\n\nSteinegger, Martin, and Johannes Söding. 2017.\n“MMseqs2 Enables Sensitive Protein Sequence Searching\nfor the Analysis of Massive Data Sets.” Nat. Biotechnol.\n35 (11): 1026–28.\n\n\nZhang, Z, S Schwartz, L Wagner, and W Miller. 2000. “A Greedy\nAlgorithm for Aligning DNA Sequences.” J.\nComput. Biol. 7 (1-2): 203–14.\n\n\nZhou, Naihui, Yuxiang Jiang, Timothy R Bergquist, Alexandra J Lee,\nBalint Z Kacsoh, Alex W Crocker, Kimberley A Lewis, et al. 2019.\n“The CAFA Challenge Reports Improved Protein Function\nPrediction and New Functional Annotations for Hundreds of Genes Through\nExperimental Screens.” Genome Biol. 20 (1): 244.",
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