Genome Browser Software Features
From genomewiki
This page contains a list of major new software features found in the UCSC Genome Browser. The most recent features are always at the top of the page.
15 May, 2009 (v206)
- Fixed a couple off-by-one problems with insertion lines on the right end of CDS
- Fixed performance/memory leak for bedList
- Fixed bug where exons within 3 bases of the start of a chromosome are rendered in solid yellow
- hgTracks cart cleanup
- Changes to details pages for displaying ENCODE metadata
- Fixed bug in hgTracks for rendering colored bars on blat and pcr results
1 May, 2009 (v205)
- Increased size for table names of composite tracks to accommodate long ENCODE table names
- New file types: bigBed and bigWig
- Initial implementation of gff3 parser
17 April, 2009 (v204)
- Fixed off-by-one error that caused blue insert line to be drawn 1 base to the left of the end of + strand items
- Fix to Table Browser schema for subtrack tables
- Fixed Table Browser to allow show schema to work properly for non-genome databases
- Set USE_SSL=0 be the default since some mirror sites have difficulty
- Added numeric field validation by javascript to hgTracks
- Added numeric field validation by javascript to Table Browser
- Extended BLAT to accept long chrom names (e.g. chrNN_something)
- Fixed many instances of Table Browser using composite table when subtrack table is needed
3 April, 2009 (v203)
- added color-by-gray-scale option to Net track configuration (in addition to existing color-by-chromosome)
- new output type in Table Browser for microarray tracks: microarray tissue names
13 March, 2009 (v202)
- changed PCR display to indicate the location of primers
27 February, 2009 (v201)
12 February, 2009 (v200)
- turned on drag-and-zoom feature by default
- fixed navigation to Ensembl when their chromosome names are different than ours
30 January, 2009 (v199)
- introduced multi-view track configuration
16 January, 2009 (v198)
- added drag-and-zoom feature to image (hgTracks)
- changed default image width from 620 pixels to 800 pixels
- added expand all / collapse all buttons for groups on hgTracks
- import marker-value pairs into Genome Graphs to get a custom marker column in the Gene Sorter
- Table Browser sped up when large number of ID names are uploaded/pasted
19 December, 2008 (v197)
- Turned on by default the "next/previous exon navigation"
5 December, 2008 (v196)
- (partial list)
- hgPcr expanded to include UCSC Genes amplification for human and mouse (jumps across introns).
18 November, 2008 (v195)
- Session tool UI changes.
- Session tool gives error message when a session is given an existing name.
- Option to not color chains in the Chain track.
- Option to filter chains in the Chain track on a particular chromosome.
31 October, 2008 (v194)
16 October, 2008 (v193)
- Added next/previous item capability to Custom Tracks.
- Added MAF r lines to indicate how MAF regions were defined.
- Automatic updates to upstream FASTA and MAF files.
3 October, 2008 (v192)
- New CGI: hgPal
22 September, 2008 (v191)
9 September, 2008 (v190)
- Added MAF as custom track type
22 August, 2008 (v189)
- Fixed snp128 and snp129, so Table Browser filter doesn't show misleading choices.
- Fixed PDF/PS output to not include hidden BLAT results.
8 August, 2008 (v188)
- Added links to other organisms' browsers and DNA from Conservation track details page.
28 July, 2008 (v187)
- Added next-item feature to BED tracks with less than 9 columns
- Always show the "hide all" button even if the track control display is turned off.
11 July, 2008 (v186)
- Display the "hide all" button even if the track control display is turned off
- Added check for custom track existence when saving a session
- Added next-item feature to BED tracks with less than 9 columns
- New link in xenoRefGene details page to browser for other species
- New "D" (DNA) link on Conservation track details page for all species
27 June, 2008 (v185)
- Position/Search box now allows a single-base search (e.g. chr3:12345)
16 June, 2008 (v184)
- Added support for MAF-formatted custom tracks.
- java script now can collapse control button groups without server round trips
Previous Releases
- Genome Browser Scale Bar (in Base Position track).