exonerate

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minimum sequence length 54bp?

3

Hi Nathan, we are working with museum samples, so lots of very short fragments. I've noticed that exonerate only uses sequences that are 54bp or longer from our data. We...

bwprice

Alignment issues with proteins containing selenocysteine

12

When I attempt to align _SELENON_ RefSeq transcript NM_020451.2 with it's corresponding protein sequence (NP_065184.2), exonerate reports: `** FATAL ERROR **: Unknown amino acid [U]` `exiting ...` This suggests that...

leicray

Hi, is there a way to set exonerate to align each input query sequences in ungapped model (which is also the default model), without considering the sequence similarity or sequence...

kkunwar

Unknown amino acid [-]

9

When "--showalignment yes" I continually get "*\* FATAL ERROR **: Unknown amino acid [-]". When "--showalignment no" it's fine. Is this a problem with the gap symbol? Thanks

jwasmuth

Merging with gff3-capable fork of 2.2.0 version?

1

Hi Nathan, 1. are you aware of this forked repo? https://github.com/hotdogee/exonerate-gff3 which is an improved version of exonerate-2.2.0 with GFF3 format output support Maybe you could unite the efforts. 2....

mmokrejs

Unclear effect of the protein2genome model

1

The manual says: "protein2genome This model allows alignment of a protein sequence to genomic DNA. This is similar to the protein2dna model, with the addition of modelling of introns and...

cmayer

Segmentation fault protein2genome

6

Hi, I'm getting this segmentation fault, and I don't know how to fix it, any help? ``` Segmentation fault exonerate --showsugar T --showtargetgff T --softmasktarget T -n 2 --model protein2genome...

francicco

Hi, I want to use exonerate to predict gene. but the result don't show the exon phase and result premature termination of the gene.here is my code exonerate -t genome.fa...

shiyi-pan