Help:How can I access the Anopheles gambiae haplotype region sequences

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First a bit of background / warning: the alternative haplotype regions would actually be better described as alternative assemblies. The sequenced PEST strain is thought to have been segregating 2 rather divergent versions/haplotypes for certain chromosome regions. The WGS sequencing reads will have come from both versions, and the assembly program seems to have generated 2 different assemblies for some of these regions. However, each of these alternative assemblies is likely to be a mosaic of segments from both versions, rather than representing a pure version of either 'haplotype'. The quality of these regions is sometimes quite poor (lots of gaps).

The lengths are displayed in ContigView eg:3L_hap_9:11046966-112165 corresponds to 3L:11046966-11206189 To see the latter, click on the red representation of the haplotype block and look in the pop-up box. Note that you can switch to a view of the alternative chromosome (ie with this alternative assembly region substituted) by taking the link in the pop-up. But we only have basic annotation (repeats, gaps, blast hits) on the alternative assembly regions. If you want the sequences to do your own alignment, you can use ExportView: http://www.ensembl.org/Anopheles_gambiae/exportview (or take the 'Export sequence as FASTA' link from the left-hand panel when you are viewing the region in ContigView.)

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