d2a02f56a0e84d51213d44955b694ce7daace230
jnavarr5
  Fri May 31 11:41:50 2019 -0700
Updating redirected links for hg18, uiLinks cronjob.

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 <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 &quot;0G&gt;3A(GTA&gt;ATA)&quot;.
 If <em>N</em> Neandertal reads match neither ancestral nor derived
 base, then a &quot;+<em>N</em>?&quot; is added before the codons
 (i.e. &quot;0G&gt;3A+N?(GTA&gt;ATA)&quot;).
 </P>
 
 <H2>Methods</H2>
 <P>
 Neandertal DNA was extracted from a ~49,000-year-old bone
 (Sidr&oacute;n 1253), which was excavated in El Sidr&oacute;n 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>