d2a02f56a0e84d51213d44955b694ce7daace230 jnavarr5 Fri May 31 11:41:50 2019 -0700 Updating redirected links for hg18, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/human/ntHumChimpCodingDiff.html src/hg/makeDb/trackDb/human/ntHumChimpCodingDiff.html index 4f443cb..0dca855 100644 --- src/hg/makeDb/trackDb/human/ntHumChimpCodingDiff.html +++ src/hg/makeDb/trackDb/human/ntHumChimpCodingDiff.html @@ -1,51 +1,51 @@ <H2>Description</H2> <P> This track displays Neandertal alleles for human-chimp protein-coding differences on the human lineage using orangutan as the outgroup to determine which allele is more likely to be ancestral. </P> <H2>Display Conventions and Configuration</H2> <P> Neandertal ancestral alleles are colored blue; derived (human) alleles are colored green. </P> <P> The item names show the number of Neandertal reads for the ancestral and derived alleles, followed by the ancestral and derived codons enclosed in parentheses. For example, if no Neandertal reads matched the ancestral base G and three Neandertal reads matched the derived base A, and the ancestral and derived codons were GTA and ATA respectively, then the item name would be "0G>3A(GTA>ATA)". If <em>N</em> Neandertal reads match neither ancestral nor derived base, then a "+<em>N</em>?" is added before the codons (i.e. "0G>3A+N?(GTA>ATA)"). </P> <H2>Methods</H2> <P> Neandertal DNA was extracted from a ~49,000-year-old bone (Sidrón 1253), which was excavated in El Sidrón cave, Asturias, Spain. Non-synonymous changes that occurred on the human lineage since the ancestral split with chimpanzee were identified by aligning human, chimpanzee and orangutan protein sequences for all orthologous proteins in <A HREF="https://www.ncbi.nlm.nih.gov/homologene" TARGET=_BLANK>HomoloGene</A> (Build 58) . Comparison of these three species allowed the assignment of human/chimpanzee differences to their respective evolutionary lineages. An Agilent custom oligonucleotide array covering the 13,841 non-synonymous changes inferred to have occurred in the human lineage was designed and used to capture Neandertal sequences. </P> <H2>Reference</H2> <p> Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z <em>et al</em>. -<a href="http://science.sciencemag.org/content/328/5979/723" target="_blank"> +<a href="https://science.sciencemag.org/content/328/5979/723" target="_blank"> Targeted investigation of the Neandertal genome by array-based sequence capture</a>. <em>Science</em>. 2010 May 7;328(5979):723-5. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20448179" target="_blank">20448179</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140021/" target="_blank">PMC3140021</a> </p>