The alignment found by the program was compared to structural overlays of sex-lethal and FIR1+2, and, accordingly, slight modifications to the alignment were manually performed in the region linking the two RRM domains to reflect the true structural alignment of those residues.
At this time, the highway had the same extent as it does today; the only changes made to the highway over the years were slight modifications to its alignment due to the straightening of connecting highways.
Further modifications to the alignment were done manually.
Modifications to sequence alignment pipelines are also needed to extract the unaligned reads after mapping to the mouse reference and remap them to the human reference.
It uses existing aligner and assembler (with minor modifications to keep all possible alignments discovered, details in Section 3.1) to identify regions to which fragments align.
We describe the profile alignment algorithm with core constraint in terms of required modifications to the canonical algorithm for local alignment (Smith and Waterman, 1981).
However, it suffers from relatively low production rates and poor control of fiber alignment without substantial modifications to the fiber collector mechanism.
We first present the algorithms used by TopHat and Cufflinks in ranking and reporting alignments and genes and then discuss our modifications to retain all fragment and partial fragment (unpaired reads) alignments.
Although GPU-BLAST shares many data structures with NCBI-BLAST, we made necessary modifications to exploit the GPU without compromising the accuracy of the produced alignments.
Manual inspection of the alignment differences (resulting, for example, from different tools, changed parameters or modifications to the reference MSA) is supported via a differencing function.
Interestingly, this was achieved without any modifications to the search algorithm itself, since the score dissection was applied to the alignments post mortem.
