TY - DATA T1 - A five-step annotation methodology was used. PY - 2013/02/20 AU - Ramy Arnaout AU - William Lee AU - Patrick Cahill AU - Tracey Honan AU - Todd Sparrow AU - Michael Weiand AU - Chad Nusbaum AU - Klaus Rajewsky AU - Sergei B. Koralov UR - https://plos.figshare.com/articles/figure/_A_five_step_annotation_methodology_was_used_/419129 DO - 10.1371/journal.pone.0022365.g001 L4 - https://ndownloader.figshare.com/files/748769 KW - five-step KW - annotation KW - methodology KW - was N2 - Step 1: New sequence was obtained through pyrosequencing. Step 2: Using a word-counting strategy, the best-match V was determined. When there was a tie for best match, or when the best match was nevertheless a poor match, sequences were removed from subsequent V-D-J usage analysis. The best-match V was then aligned to the new sequence using megablast. Steps 3: The region that matched V was removed (grayed out in the figure) and the same word-counting strategy was applied to the remaining sequence to determine the best-match J sequence. As with V, ties and poor matches were removed; the best-match J was aligned using megablast. Step 4: The region that matched J was removed (gray) and D was assigned and aligned to the remainder as in Steps 2 and 3. Step 5: Using the alignments, exonucleotide chewback and nucleotide addition were determined. ER -