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The Look The length hits the knee, like this Max Mara sportif shorts-suit.
We filtered the low coverage (<60 % coverage of the protein length) hits.
We were especially interested in full length hits of the TC sequences vs. known proteins.
The functionality of these transposons is not known, however, nearly full length hits to the gag-pol polyprotein nucleotide sequence were found on BACs 77-G20 and 74-F12 74-F12
We complemented this approach with an analysis in which 1,000 transcripts were sorted by length, hits counted at each position and scaled to the maximum value for each transcript, and the data plotted as a two dimensional heat map.
Similarly, in a BLASTp analysis of the pennycress predicted peptides against a single database containing all five Brassicaceae species, 15,414 predicted pennycress peptides had highly similar (e ≤ 1 × 10−5 and ≥70% hit length) hits to E. salsugineum (Supplementary Dataset S6).
Similar(53)
wBol1_1092 has full-length hits to multiple secA proteins in the jumping ant Harpegnathos saltator, and a near-full length hit to a hypothetical protein in Daphnia pulex.
Only the best BLAST (minimum e-value, maximum length) hit from each contig was extracted.
FLOCOs are defined as TC sequences that have an (almost) full length hit against a known protein.
These sets of proteins were put through blast (tblastn, 40% homology and 40% length hit) in a sequential order against the rest of the C. concisus genomes.
A BLAST query using a 135-nucelotide segment (chr6: 32609874–32610008) harboring the SNP site (chr6: 32609965) from the HLA-DQA1*03 03 HLA-DQA1*03 03 the top full length hit locallelet the exon 3 of the HLA-DQA2 gene.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com