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SLAST: Simple Local Alignment Search Tool

Bermudez, J.

2019-11-15 bioinformatics
10.1101/840546 bioRxiv
Show abstract

We present a local alignment search tool not based on the usual strategy of seed and grow often employed for these tools. Instead, we just find regions in the database sequences having a high density of seed matches and then we perform a Smith-Waterman local alignment of the query sequence into these regions. This approach has some advantages for some use cases.

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
PLOS ONE
● 5266 papers in training set
Top 11%
17.1%
Similar papers in this journal
2
BMC Bioinformatics
○ 457 papers in training set
Top 0.4%
13.0%
Similar papers in this journal
3
Bioinformatics
◐ 1204 papers in training set
Top 3%
7.9%
Similar papers in this journal
4
PeerJ
◐ 308 papers in training set
Top 0.3%
7.9%
Similar papers in this journal
5
PLOS Computational Biology
● 1863 papers in training set
Top 6%
5.5%
50% of probability mass above
6
F1000Research
○ 88 papers in training set
Top 0.2%
5.5%
Similar papers in this journal
7
Journal of Open Source Software
● 25 papers in training set
Top 0.1%
5.5%
8
Bioinformatics Advances
◐ 203 papers in training set
Top 1%
4.1%
9
GigaScience
◐ 212 papers in training set
Top 0.8%
4.1%
10
Journal of Bioinformatics and Systems Biology
○ 15 papers in training set
Top 0.1%
2.7%
11
Journal of Computational Biology
○ 48 papers in training set
Top 0.7%
1.4%
12
Scientific Reports
○ 3612 papers in training set
Top 60%
1.3%
13
Gigabyte
● 62 papers in training set
Top 0.8%
1.1%
14
IEEE/ACM Transactions on Computational Biology and Bioinformatics
● 38 papers in training set
Top 0.8%
1.1%
15
Journal of Molecular Evolution
○ 22 papers in training set
Top 0.3%
1.1%
16
Frontiers in Bioinformatics
○ 49 papers in training set
Top 1%
1.0%
17
BMC Genomics
○ 406 papers in training set
Top 7%
1.0%
18
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 4%
1.0%
19
Biology Methods and Protocols
◐ 61 papers in training set
Top 2%
0.8%
20
Briefings in Bioinformatics
◐ 354 papers in training set
Top 7%
0.8%
21
Frontiers in Genetics
○ 230 papers in training set
Top 6%
0.6%
22
Biology
○ 45 papers in training set
Top 1%
0.6%
23
Ecology and Evolution
○ 267 papers in training set
Top 6%
0.6%
24
eLife
● 5828 papers in training set
Top 70%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.