Sentence examples for removed sequences were from inspiring English sources
Briefly, low quality (removed, sequences were aligned against an orangutan (P. abelii) genome (3 ), and nonmapped sequences were subjected to de novo assembly.
Other removed sequences were determined on the basis of a blastn homology search against the integrated ESTs (E < 1.0e-50 1.0e-50ibosomal RNA and organelle DNA query sequences (DDBJ/EMBL/GenBank accession: AF174629, AF206999, AF479118, AJ006440, AP000423, X52322, Y08501, Y08502, AF162215, AF168884, AF274652).
The majority of removed sequences were identical or nearly-identical to human sequences and two sequences were recognized by the MG-RAST as chimeras.
While some fragmented sequences are removed, which helps with alignment performance by limiting the number of gaps in the MSA [4], the majority of the removed sequences are simply highly similar (greater than 95%) and therefore redundant.
We then further removed sequences that were read only once and 6,870,535 reads remained.
These were then filtered to remove sequences that were unlikely to represent U1/U2 introns (see Materials and Methods).
A total of 5.2 × 107 bases from 15,560 cleaned (redundancy removed) sequence documents were analyzed.
After redundancy was removed, sequences ≥ 18 nt were mapped to the human genome (UCSC hg18) using SOAP.
MUSCLE alignments were inspected visually to remove sequences that were obvious alignment errors.
Adaptors were removed, and sequences were trimmed for length and quality with standard settings.
Priming sites were manually removed and sequences were manually aligned in Mesquite 2.72 [ 69].
