Liftoff
An accurate GFF3/GTF lift over pipeline (by agshumate)
miniprot
Align proteins to genomes with splicing and frameshift (by lh3)
| Liftoff | miniprot | |
|---|---|---|
| 2 | 1 | |
| 395 | 305 | |
| - | - | |
| 5.2 | 5.8 | |
| 10 months ago | about 2 months ago | |
| Python | C | |
| GNU General Public License v3.0 only | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Liftoff
Posts with mentions or reviews of Liftoff.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-02-06.
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Identifying potential genes involved in nociception
How distant is your study organism to Drosophila? You mention it's another model organism but I can't think of any others that are close to flies. If you have a close-ish organism you could try a 'lift' of the annotations from Drosophila to your draft genome (I like 'liftoff' for this). This tries to match across genes from your input reference (Drosophila) to your draft genome. This works best when the 2 organisms are somewhat closely related. You can then look up where those 'painless' genes in your draft organism's reference, and this info can also be used to inform your transcriptome analysis.
- Cross-species functional annotation?
miniprot
Posts with mentions or reviews of miniprot.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-02-06.
-
Identifying potential genes involved in nociception
Alternatively, there is a new tool out from Heng Li (bioinformatics godfather) which apparently does good quality mapping of proteins to references (miniprot). You could download your 'painless' genes from Drosophila and use this tool to look for them in your reference (similar to above, except this tool is apparently better able to handle larger differences).
What are some alternatives?
When comparing Liftoff and miniprot you can also consider the following projects:
Augustus - Genome annotation with AUGUSTUS
seqtk - Toolkit for processing sequences in FASTA/Q formats
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences