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The first look at annotations for the new Rat Genome Sequence Assembly, RGSC 5.0, is now available on the UCSC genome browser! Utilizing their automated alignment pipelines, researchers at the UCSC database have produced a preliminary set of tracks by "BLATing" existing sequences, such as RefSeq RNAs for rat and other species, against the sequence of the new assembly. NCBI's and Ensembl's annotations for the new assembly (i.e. placement of genomic elements and gene predictions) are expected out within the next few months. As has been seen in the past, inconsistencies, even sometimes substantial inconsistencies, are to be expected among the major annotation groups (UCSC, NCBI, Ensembl) due to the differences in annotation methods, but RGD is committed to providing access to all the available information in order to give users a complete picture of the data. Click here to get your first look at the new assembly. Want to see where your favorite sequence has moved to? RGSC 5.0 is also available in UCSC's BLAT tool. Click here to try it out. Finally, if you are concerned that the data you have been using that was derived from the RGSC 3.4 genome assembly will be lost, rest assured that UCSC's tools still include the 3.4 assembly and its annotations. When you are on the UCSC page, click the dropdown list for "assembly" to choose between the 5.0 (the new default) and the 3.4 assemblies. And even after the transition has been fully completed, RGD will continue to provide the "old" assembly data in our web pages, tools and ftp files. |
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