Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Martin Larralde
pyrodigal
Commits
fd822bce
Commit
fd822bce
authored
Feb 25, 2022
by
Martin Larralde
Browse files
Reword some sentences in `paper.md`
parent
e7028196
Changes
1
Hide whitespace changes
Inline
Side-by-side
paper/paper.md
View file @
fd822bce
...
...
@@ -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
\a
utoref{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:
-
$(T_i = STOP)
\l
and (T_j
\n
e STOP)
\l
and (S_i = S_j)$
...
...
@@ -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
bypass
ing
the scoring of invalid
connection.
first pass produces a look-up table
used to
bypass the scoring of invalid
connection
s
.
The performance of the connection scoring was evaluated on 50 bacterial
sequences of various length, as shown in
\a
utoref{fig:benchmark}. It suggests
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment