Commit fd822bce authored by Martin Larralde's avatar Martin Larralde
Browse files

Reword some sentences in `paper.md`

parent e7028196
......@@ -114,9 +114,8 @@ There are pairs of codons between which a gene can never span, such as two
stop codons, or a forward start codon and a reverse stop codon, as shown in
\autoref{fig:method}. Upon inspection, we realized the `score_connections`
was still called in invalid cases that could be labelled as such beforehand.
Identifying these invalid connections is done by checking the strand, type and
reading frame of the pair of nodes. Considering two nodes $i$ and $j$, the
Identifying these invalid connections is feasible by checking the strand, type
and reading frame of a node pair. Considering two nodes $i$ and $j$, the
connection between them is invalid if any of these boolean equations is true:
- $(T_i = STOP) \land (T_j \ne STOP) \land (S_i = S_j)$
......@@ -136,8 +135,8 @@ Since all these attributes have a small number of possible values
$-1$, $-2$, $-3$, $+1$, $+2$, $+3$ for the frame), they can all be stored in
a single byte. Using the SIMD features of modern CPUs allows processing several
nodes at once (8 nodes with NEON and SSE2 features, 16 nodes with AVX2). This
first pass produces a look-up table that allows bypassing the scoring of invalid
connection.
first pass produces a look-up table used to bypass the scoring of invalid
connections.
The performance of the connection scoring was evaluated on 50 bacterial
sequences of various length, as shown in \autoref{fig:benchmark}. It suggests
......
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