Aedes aegypti (LVP_AGWG) vs Anopheles gambiae LastZ Results
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Aedes aegypti (LVP_AGWG) (Aedes aegypti, AaegL5) and Anopheles gambiae (Anopheles gambiae, AgamP4) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release . Aedes aegypti (LVP_AGWG) was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.
Results
Number of alignment blocks: 62,044
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Aedes aegypti |
Uncovered: 1,255,804,357 out of 1,278,732,104 |
Uncovered: 6,552,476 out of 24,249,714 |
| Anopheles gambiae |
Uncovered: 251,088,590 out of 273,109,044 |
Uncovered: 4,706,730 out of 21,473,329 |
Configuration parameters
| Parameter | Value |
|---|---|
| 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
|
| Other parameters (other) | --ambiguous=iupac |
Chunking parameters
| Aedes aegypti (LVP_AGWG) | Anopheles gambiae | |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
