198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/makeDb/trackDb/cow/bosTau6/numtSeq2012.html src/hg/makeDb/trackDb/cow/bosTau6/numtSeq2012.html index 3b6aa6f5ecb..82304877aac 100644 --- src/hg/makeDb/trackDb/cow/bosTau6/numtSeq2012.html +++ src/hg/makeDb/trackDb/cow/bosTau6/numtSeq2012.html @@ -1,112 +1,112 @@ <h2>Description and display conventions</h2> <p> <b>NumtS</b> (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear genomic sequences. The most credited hypothesis concerning their generation suggests that in the presence of mutagenic agents, or under stress conditions, fragments of mtDNA escape from mitochondria, reach the nucleus and insert into chromosomes during break repair; although NumtS can also derive from duplication of genomic fragments. NumtS may be a cause of contamination during mtDNA sequencing and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group chaired by M. Attimonelli (University of Bari, Italy) has produced the RPNumtS (Reference Cow NumtS) compilation annotating Cow assembled NumtS. To allow the scientific community to access the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the group has designed the Cow NumtS tracks described below. </p> <p> The NumtS tracks show nuclear and mitochondrial regions, based on the High Score Pairs (HSPs) obtained by aligning the mitochondrial reference genome (NC_006853) with the bosTau6 assembly of the cow genome. </p> <ol> <li><b>"NumtS (Nuclear mitochondrial Sequences)" Track</b> <p> The "NumtS mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear genome. The shading of the items reflect the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the mitochondrial mapping is provided, thus allowing easier cross referencing between the NumtS subtracks. </p> </li> <li><b>"NumtS assembled" Track</b> <p> The "NumtS assembled" track shows items obtained by assembling HSPs annotated in the "NumtS" track fulfilling the following conditions: <ul> <li>The orientation of their alignments must be concordant.</li> <li>The distance between them must be less than 2 kb, on the mitochondrial genome as well as on the nuclear genome.</li> </ul> <p> Exceptions for the second condition arise when a long repetitive element is present between two HSPs. </p> </li> <li><b>"NumtS on mitochondrion" Track</b> <p> The "NumtS on mitochondrion" track shows the mapping of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the nuclear mapping is provided. </p> <li><b>"Cow NumtS on mitochondrion SNP" Track</b> <p> The "Cow NumtS SNP" shows the mapping of the HSPs on the mitochondrial genome, with the SNPs which fall within, derived from comparison with the bosTau6 assembly. No shading is provided here. </p> </ol> <h2>Methods</h2> <p> NumtS mappings were obtained by running Blast2seq (program: BlastN) between each chromosome of the Cow Genome (bosTau6 assembly) and the Cow mitochondrial reference sequence (AC: NC_006853), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with spreadsheet interpolation and manual inspection. BED format is used for the first three annotation tracks, while for the last one the SAM/BAM format is preferred. </p> <h2>Credits</h2> <p> These data were provided by Francesco Maria Calabrese, Dario Leonardo Balacco, Domenico Simone -and Marcella Attimonelli from the Department of of Biosciences, Biotechnology and Pharmacological +and Marcella Attimonelli from the Department of Biosciences, Biotechnology and Pharmacological Sciences (University of Bari, Italy). Manual inspection and format details have been carried out by Francesco Maria Calabrese, Dario Leonardo Balacco and Domenico Simone. </p> <h2>References</h2> <p> Calabrese FM, Simone D, Attimonelli M. <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-S4-S15" target="_blank">Primates and mouse NumtS in the UCSC Genome Browser</a>. <em>BMC Bioinformatics</em>. 2012 Mar 28;13 Suppl 4:S15. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22536961" target="_blank">22536961</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3314570" target="_blank">PMC3314570</a> </p> <p> Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-267" target="_blank"> The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS</a>. <em>BMC Genomics</em>. 2008 Jun 3;9:267. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18522722" target="_blank">18522722</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447851" target="_blank">PMC2447851</a> </p> <p> Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-517" target="_blank"> The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser</a>. <em>BMC Genomics</em>. 2011 Oct 20;12:517. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22013967" target="_blank">22013967</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228558" target="_blank">PMC3228558</a> </p>