File Changes for steve

v260_preview2 to v260_base (2011-11-22 to 2011-12-06) v260

• src/hg/htdocs/FAQ/FAQdownloads.html
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    Changed mailto:genome@soe.ucsc.edu link in the 'Converting genome coordinates between assemblies' section to point to the Contacts page
• src/hg/makeDb/genbank/etc/rr.dbs
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    Added gorGor3 and nomLeu1
• src/hg/makeDb/trackDb/all_est.html
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    Full text of BLAT article is now free. Changed the URL from abstract to full. Also updated 'Genbank: update' URL
• src/hg/makeDb/trackDb/all_mrna.html
  • lines changed 2, context: html, text, full: html, text
    Full text of BLAT article is now free. Changed the URL from abstract to full. Also updated 'Genbank: update' URL
• src/hg/makeDb/trackDb/est.html
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    Full text of BLAT article is now free. Changed the URL from abstract to full.
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
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    Moved a period from inside to outside a link
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    Removed '.2' and the note about version numbers from the sample query since the query including version numbers causes an error on beta and the RR
• src/hg/makeDb/trackDb/gorilla/gorGor3/description.html
  • lines changed 4, context: html, text, full: html, text
    Removed the trailing '.2' from the sample queries because they caused an error when searching with the. Removed unnecessary period from a URL.
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    Removed a period from inside a link
• src/hg/makeDb/trackDb/human/encodeEgaspFull.html
  • lines changed 14, context: html, text, full: html, text
    Fixed a broken link and updated various outdated links
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    Changed genome.imim.es to genome.crg.es
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    Changed Aceview to AceView
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    Changed 'Jigsaw' to 'JIGSAW'
• src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
  • lines changed 46, context: html, text, full: html, text
    Fixed broken link and updated several outdated linkes
• src/hg/makeDb/trackDb/human/hapmapSnps.html
  • lines changed 15, context: html, text, full: html, text
    Fixed a broken link. Updated some outdated links.
• src/hg/makeDb/trackDb/human/hg16/encodeMlaganAlign.html
  • lines changed 17, context: html, text, full: html, text
    Removed a link that was no longer valid. Updated some outdated links.
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    Corrected journal citation format
  • lines changed 7, context: html, text, full: html, text
    Corrected journal citation format
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    Re-italicized et al.
• src/hg/makeDb/trackDb/human/hg16/hg17Kg.html
  • lines changed 18, context: html, text, full: html, text
    Fixed a broken link. Updated some outdated links.
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    Changed link to point directly to UniProt
• src/hg/makeDb/trackDb/human/hg17/encodeGisChipPetAll.html
  • lines changed 3, context: html, text, full: html, text
    Fixed broken link and updated some outdated links
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    Removed comma before et. al.
• src/hg/makeDb/trackDb/human/hg17/encodeMlaganAlign.html
  • lines changed 16, context: html, text, full: html, text
    Removed a link that was no longer valid. Updated some outdated links.
  • lines changed 7, context: html, text, full: html, text
    Corrected journal citation format
  • lines changed 2, context: html, text, full: html, text
    Re-italicized et al.
• src/hg/makeDb/trackDb/human/hg17/encodeTbaAlign.html
  • lines changed 18, context: html, text, full: html, text
    Corrected journal citation format
  • lines changed 5, context: html, text, full: html, text
    Re-italicized et al.
• src/hg/makeDb/trackDb/human/hg17/encodeUppsalaChip.html
  • lines changed 6, context: html, text, full: html, text
    Fixed a broken link. Updated some outdated links. Corrected citation format.
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    Updated an outdated link.
• src/hg/makeDb/trackDb/human/hg17/encodeUppsalaChipBut.html
  • lines changed 56, context: html, text, full: html, text
    Fixed a broken link. Updated some outdated links. Corrected citation format.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipRfbr.html
  • lines changed 6, context: html, text, full: html, text
    Fixed a broken link. Updated an outdated link.
• src/hg/makeDb/trackDb/human/hg17/knownGene.html
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    Fixed a broken link and updated some outdated links
• src/hg/makeDb/trackDb/human/hg17/retroposons.html
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    Removed broken link. Created link to Roswell Park Cancer Institute. Updated outdated links.
• src/hg/makeDb/trackDb/human/hg17/sangamoDnaseHs.html
  • lines changed 13, context: html, text, full: html, text
    Fixed a broken link and updated some outdated links
• src/hg/makeDb/trackDb/human/hg17/snpArray.html
  • lines changed 4, context: html, text, full: html, text
    Fixed broken links
• src/hg/makeDb/trackDb/human/hg18/knownGene.html
  • lines changed 14, context: html, text, full: html, text
    Fixed a broken link and updated some outdated links
• src/hg/makeDb/trackDb/human/hg18/stsMap.html
  • lines changed 7, context: html, text, full: html, text
    Fixed a broken link and updated some outdated links
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisChipPetAll.html
  • lines changed 8, context: html, text, full: html, text
    Fixed a broken link and updated some outdated links
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • lines changed 2, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
  • lines changed 4, context: html, text, full: html, text
    Fixed a broken link and updated an outdated link
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 62, context: html, text, full: html, text
    Changed ordering of organisms in placental and vertebrate section
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    Changed gorGor1 to gorGor3 and added nomLeu1 to primate section
• src/hg/makeDb/trackDb/human/perlegen.html
  • lines changed 9, context: html, text, full: html, text
    Perlegen Sciences is no longer in business, so removed links. Also updated the journal link.
• src/hg/makeDb/trackDb/human/stsMap.html
  • lines changed 6, context: html, text, full: html, text
    Updated some outdated links
• src/hg/makeDb/trackDb/human/vistaEnhancers.html
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    Fixed a broken link and updated some outdated links
• src/hg/makeDb/trackDb/intronEst.html
  • lines changed 1, context: html, text, full: html, text
    Full text of BLAT article is now free. Changed the URL from abstract to full.
• src/hg/makeDb/trackDb/knownGene.html
  • lines changed 19, context: html, text, full: html, text
    Fixed a broken link and updated some outdated links
  • lines changed 1, context: html, text, full: html, text
    Made a correction regarding UniProt
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    Made corrections regarding UniProt
• src/hg/makeDb/trackDb/mouse/mm7/knownGene.html
  • lines changed 23, context: html, text, full: html, text
    Fixed a broken link and updated some outdated links
• src/hg/makeDb/trackDb/mrna.html
  • lines changed 1, context: html, text, full: html, text
    Full text of BLAT article is now free. Changed the URL from abstract to full.
• src/hg/makeDb/trackDb/refGene.html
  • lines changed 1, context: html, text, full: html, text
    Full text of BLAT article is now free. Changed the URL from abstract to full.
• src/hg/makeDb/trackDb/xenoMrna.html
  • lines changed 1, context: html, text, full: html, text
    Full text of BLAT article is now free. Changed the URL from abstract to full.
• src/hg/makeDb/trackDb/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    Full text of journal article is now free. Changed the URL from abstract to full.