miniprot
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lh3
Align proteins to genomes with splicing and frameshift
Dear @lh3 , Thanks for developing miniprot. I have been trying it out & it is extremely useful. I had an idea for a possible enhancement... it would be very...
When aligning proteins to a chromosome with large size (maybe greater than 2Gb), the output gff file is almost empty. 
Hi, I was using miniprot to align one protein in Sorghum to maize genome, but no matter how I changed the parameters, only one alignment was returned. But if I...
It just comes to me that miniprot might be used to identify homologous TEs (based on evolutionary distant TE protein sequence) because many TEs have conserved domains (and structures) although...
What would be a recommended setting for a slower but more sensitive alignment to distant homologues?
Hi, I get the following error when running miniprot looking for 200 proteins at a 73MB genome: [M::[email protected]*1.01] read 68163509 bases in 69053 contigs [M::[email protected]*1.01] 608218 blocks [M::[email protected]*2.83] collected syncmers...
When aligning proteins with paralogs located in a cluster, `miniprot` produces alignments encompassing two or more distinct genes. For example, aligning mouse protein NP_001036176.1 to human chromosome 1 (NC_000001.11) returns...
Hello, The extracted protein sequences of miniprot contains internal stop codons. Is there a way to filter out those genes coding for internal stop codons or retain only the complete...
When I use these parameters: ``` ./miniprot -G 100 -O 10 -J 34 -F 30 --gff -ut32 nucleotide.fasta proteins.fasta ``` I get very close variants of the same alignment: ```...
I noticed this when testing for #33. In the example shown below, the `cs:Z:` tag uses the following to represent an intron: `~gt-1ag`. Is this expected? ```bash $ efetch -db...