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<h1>Analysis tools</h1>
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</div>
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</section>
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<h2 id="use-the-ncbi-toolkit-to-compare-">Use the NCBI Toolkit to compare genomic sequences</h2>
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<h3 id="blast">BLAST</h3>
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<p>Find regions of similarity between biological sequences with the
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<a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?LINK_LOC=CGR">Basic Local Alignment Search Tool (BLAST)</a>.
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There are many ways to BLAST:</p>
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<ul>
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<li><a href="https://blast.ncbi.nlm.nih.gov/smartblast/?LINK_LOC=CGR">SmartBLAST</a>: find proteins highly similar to your query </li>
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<li><a href="https://www.ncbi.nlm.nih.gov/tools/primer-blast/?LINK_LOC=CGR">Primer-BLAST</a>: design primers specific to your PCR template </li>
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<li><a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=blastn&BLAST_SPEC=GlobalAln&LINK_LOC=CGR">Global Alignment</a>: compare two sequences across their entire span </li>
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</ul>
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<h3 class="new-feature" id="try-the-blast-experimental-clust">Try the BLAST experimental ClusteredNR database</h3>
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<p>Identify sequences of interest faster and more efficiently across a wider range of proteins, organisms, and
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evolutionary distances using our new
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<a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=CGR">ClusteredNR database</a>.
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ClusteredNR is derived from the default BLASTP nr database with sequences clustered within 90% identity and 90% length
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to each other. </p>
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<h2 id="use-the-ncbi-toolkit-to-visualiz">Use the NCBI Toolkit to visualize data</h2>
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<h3 id="explore-genome-data">Explore genome data</h3>
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<p>Analyze annotated eukaryotic genome assemblies across the tree of life with NCBI’s web-based genome browser,
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/">Genome Data Viewer (GDV)</a>. You can add BLAST results, custom data,
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or content from Track Hubs to the display, and download slices of annotation data and high-quality graphics for
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publication directly from the browser. </p>
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<h3 id="align-sequences">Align sequences</h3>
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<p>Display and analyze multiple nucleotide or protein sequence alignments to highlight regions of sequence similarity and
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differences using the <a href="https://www.ncbi.nlm.nih.gov/projects/msaviewer/">Multiple Sequence Alignment (MSA) Viewer</a>.
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MSA Viewer's display is easily customizable to show only the alignments and metadata you need and is perfectly paired
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with BLAST- and COBALT-based analyses.</p>
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<h3 class="new-feature" id="compare-genomic-structures">Compare genomic structures</h3>
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<p>Compare assembled genomes and easily identify genomic changes that may be significant to biology and evolution with
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CGR’s new <a href="https://ncbi.nlm.nih.gov/genome/cgv/?utm_source=nih_cgr&utm_medium=referral&utm_campaign=cgv-beta-20220705">Comparative Genome Viewer</a>
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(CGV). View assembly-assembly comparisons from more than 50 annotated genomes at
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||
the whole genome, chromosome, or chromosome-region levels. </p>
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||
<p>Citation: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11101090/">The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments</a></p>
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<h2 id="need-some-help">Need some help?</h2>
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<p><a href="mailto:cgr@nlm.nih.gov">Contact us</a> for customer service support</p>
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