PMC:1892782 / 34321-35704
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1892782","sourcedb":"PMC","sourceid":"1892782","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1892782","text":"A blast search with E \u003c 1e - 10 against NonCode [20], Rfam [21], mirBase [22] and snoRNA-LBME-db [23] identified only 248 unique known ncRNA loci in human. (Note, that tRNAs and most snRNAs are multi-copy genes and hence were deliberately excluded from the data in [2]). To compare strand predictions of EvoFold with RNAstrand the multiz8way alignments of 202 loci, which are completely covered by a blast hit, were reconstructed. The majority (177) were identified to be miRNA precursors as most of the EvoFold predictions in ref. [2] are short conserved hairpins. The direction of the blast hit indirectly determines the strand of the known ncRNA when it is compared to the strand prediction of EvoFold. For 14 (13 miRNAs and 1 U6atac) loci the multiple alignments could not be reconstructed. The remaining 188 alignments were realigned and all which did not meet the prerequisites of RNAstrand were discarded: 15 alignments were shorter than the minimum length for which RNAstrand was trained with, 5 alignments had a mean pairwise identity smaller than 50%, and one alignment contained of too many gaps. This leaves 167 alignments for which the strand prediction of RNAstrand is compared to the strand prediction of EvoFold. Alignments containing more than 6 sequences were reduced to 6 sequences by rnazWindow.pl which optimizes the final alignment for a mean pairwise identity.","tracks":[{"project":"2_test","denotations":[{"id":"17540014-15608158-1690059","span":{"begin":49,"end":51},"obj":"15608158"},{"id":"17540014-15608160-1690060","span":{"begin":60,"end":62},"obj":"15608160"},{"id":"17540014-14681370-1690061","span":{"begin":74,"end":76},"obj":"14681370"},{"id":"17540014-16381836-1690062","span":{"begin":98,"end":100},"obj":"16381836"},{"id":"17540014-16628248-1690063","span":{"begin":266,"end":267},"obj":"16628248"},{"id":"17540014-16628248-1690064","span":{"begin":533,"end":534},"obj":"16628248"}],"attributes":[{"subj":"17540014-15608158-1690059","pred":"source","obj":"2_test"},{"subj":"17540014-15608160-1690060","pred":"source","obj":"2_test"},{"subj":"17540014-14681370-1690061","pred":"source","obj":"2_test"},{"subj":"17540014-16381836-1690062","pred":"source","obj":"2_test"},{"subj":"17540014-16628248-1690063","pred":"source","obj":"2_test"},{"subj":"17540014-16628248-1690064","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#dc93ec","default":true}]}]}}