EMBL-EBI User Survey 2024

Do data resources managed by EMBL-EBI and our collaborators make a difference to your work?

Please take 10 minutes to fill in our annual user survey, and help us make the case for why sustaining open data resources is critical for life sciences research.

Survey link: https://www.surveymonkey.com/r/HJKYKTT?channel=[webpage]

Nasonia vitripennis (Jewel wasp, AsymCx) vs Bombus impatiens (Common eastern bumblebee) LastZ results

Nasonia vitripennis (Jewel wasp, AsymCx) (Nasonia vitripennis, Nvit_psr_1.1) and Bombus impatiens (Common eastern bumblebee) (Bombus impatiens, BIMP_2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 106. Nasonia vitripennis (Jewel wasp, AsymCx) was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterNasonia vitripennis (Jewel wasp, AsymCx)Bombus impatiens (Common eastern bumblebee)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 67,139 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Nasonia vitripennis (Jewel wasp, AsymCx)

Uncovered: 273,402,235 out of 297,309,692
Covered: 23,907,457 out of 297,309,692

Uncovered: 7,979,760 out of 22,806,936
Matches: 9,952,057 out of 22,806,936
Mismatches: 4,485,019 out of 22,806,936
Insertions: 390,100 out of 22,806,936
Identity over aligned base-pairs: 67.1%

Bombus impatiens (Common eastern bumblebee)

Uncovered: 224,906,719 out of 246,856,484
Covered: 21,949,765 out of 246,856,484

Uncovered: 4,832,625 out of 18,806,354
Matches: 9,502,174 out of 18,806,354
Mismatches: 4,185,864 out of 18,806,354
Insertions: 285,691 out of 18,806,354
Identity over aligned base-pairs: 68.0%

Block size distribution

Size range All 67,139 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
316
2.0 kb
10 bp - 100 bp
11,445
742.3 kb
3,628
241.0 kb
100 bp - 1 kb
49,522
15.8 Mb
13,129
4.3 Mb
1 kb - 10 kb
5,855
10.0 Mb
5,534
15.8 Mb
10 kb - 100 kb
1
11.7 kb
362
6.2 Mb
100 kb - 1 Mb
1
119.7 kb