fbe36917fa06d2ce0148760497a2d821efaf9ba0 lrnassar Wed Nov 6 10:25:48 2019 -0800 Adding a link to FAQ genes page no RM diff --git src/hg/makeDb/trackDb/refGene.html src/hg/makeDb/trackDb/refGene.html index eb61828..9ebce4a 100644 --- src/hg/makeDb/trackDb/refGene.html +++ src/hg/makeDb/trackDb/refGene.html @@ -1,92 +1,96 @@ <h2>Description</h2> <p> The RefSeq Genes track shows known $organism protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly.</p> <p> Please visit the <a href="https://www.ncbi.nlm.nih.gov/projects/RefSeq/update.cgi" target="_blank">Feedback for Gene and Reference Sequences (RefSeq)</a> page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. </p> +<p> +For more information on the different gene tracks, see our <a target=_blank +href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p> + <h2>Display Conventions and Configuration</h2> <p> This track follows the display conventions for <a href="../goldenPath/help/hgTracksHelp.html#GeneDisplay" target="_blank"> gene prediction tracks</a>. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark). </p> <p> The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. <ul> <li><b>Label:</b> By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely.</li> <li><b>Codon coloring:</b> This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the <em>genomic codons</em> option from the <em>Color track by codons</em> pull-down menu. For more information about this feature, go to the <a href="../goldenPath/help/hgCodonColoring.html" TARGET="_blank"> Coloring Gene Predictions and Annotations by Codon</a> page.</li> <li><b>Hide non-coding genes:</b> By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box.</li> </ul> </p> <h2>Methods</h2> <p> RefSeq RNAs were aligned against the $organism genome using BLAT. Those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept. </p> <h2>Credits</h2> <p> This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI <a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank">RefSeq project</a>. </p> <h2>References</h2> <p> Kent WJ. <a href="https://genome.cshlp.org/content/12/4/656.full" target="_blank"> BLAT - the BLAST-like alignment tool</a>. <em>Genome Res.</em> 2002 Apr;12(4):656-64. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11932250" target="_blank">11932250</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/" target="_blank">PMC187518</a> </p> <p> Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM <em>et al</em>. <a href="https://academic.oup.com/nar/article/42/D1/D756/1051112/RefSeq-an-update-on-mammalian-reference-sequences" target="_blank"> RefSeq: an update on mammalian reference sequences</a>. <em>Nucleic Acids Res</em>. 2014 Jan;42(Database issue):D756-63. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24259432" target="_blank">24259432</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965018/" target="_blank">PMC3965018</a> </p> <p> Pruitt KD, Tatusova T, Maglott DR. <a href="https://academic.oup.com/nar/article/33/suppl_1/D501/2505241/NCBI-Reference-Sequence-RefSeq-a-curated-non" target="_blank"> NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins</a>. <em>Nucleic Acids Res.</em> 2005 Jan 1;33(Database issue):D501-4. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15608248" target="_blank">15608248</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539979/" target="_blank">PMC539979</a> </p>