The phrase "a revised sequence" is correct and usable in written English.
It can be used when referring to a modified or updated order of items, events, or processes.
Example: "After reviewing the feedback, we implemented a revised sequence for the project timeline to improve efficiency."
Alternatives: "an updated order" or "a modified arrangement".
In comparison to the L er-0 draft, the L er-0 revised sequence is a better reference (table 2).
Following Gorodkin et. al.'s lead of including gap characters in their revised Sequence Logo formulation [ 7], we have added a gap character to the Ambiscript Mosaic notation that was not present in the original Ambiscript font.
Our study emphasizes the importance of refining genome annotation as revised sequence information becomes available.
We then realigned the reads against the revised sequence.
Similarly, seven gaps were present when L er-0 whole-genome reads were aligned to the revised sequence.
Therefore, a revised 520 amino acid protein based on coding sequence from 8 exons is described in this study (see Additional File 1: revised sequence for LOC241768).
The absence of misassembly signatures overall demonstrates that the L er-0 revised sequence is superior to the draft sequence.
Revised sequence alignments were then submitted to Protest online server version 2.4 [ 36] available at http://darwin.uvigo.es/software/prottest_server.html, in order to select the appropriate protein evolution model according to our dataset.
From the stringent alignment of locus-specific reads to the L er-0 revised sequence, seven gaps were identified (six gaps corresponding to unamplified regions and one gap to the aforementioned unresolved region).
Finally, the revised sequences were compared with all the DyP sequences (a total of 218) from the 114 basidiomycete (Agaricomycotina) genomes currently (7 December 2014) sequenced and annotated at JGI, which are available at the MycoCosm portal (http://genome.jgi-psf.org/programs/fungi).
