Timeline for Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average
Current License: CC BY-SA 4.0
10 events
| when toggle format | what | by | license | comment | |
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| Aug 22, 2023 at 2:49 | history | edited | M__♦ |
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| Jun 27, 2023 at 2:36 | answer | added | M__♦ | timeline score: 1 | |
| Jun 26, 2023 at 17:48 | comment | added | Sudoh | Not a problem, doing global alignment on a phylogeny that spans a billion-years was a gamble to begin with. I am grateful you took the time to look at it. I suspect these homo-logs are not real or if they are then the global alignment algorithms we have might not be ready to work on something a phylogeny this deep. | |
| Jun 26, 2023 at 17:22 | comment | added | Sudoh | The first 8 sequences, containing both 'working' vs 'issue' sequences are here. It's a fork of Firefox send, I can use something else if you are uncomfortable with that. By locus if you mean alternate splicing then it is possible that that is what is at play. | |
| Jun 26, 2023 at 16:35 | comment | added | M__♦ | I don't want to wade through 5K sequences. What I am really asking for is a reproducible example. The example provided doesn't help understand the issue, it's the input into pal2nal I'm looking for. What I want to do is compare the input vs the output. | |
| Jun 26, 2023 at 16:22 | comment | added | Sudoh | I am happy to provide the original data, it's all open-source. Do you have a preferred way to receive them? | |
| Jun 26, 2023 at 13:32 | comment | added | M__♦ | I can see whats happening that the 'issue' sequence is a locus within the full gene for Acacia spp.. The thing is I can't see the original sequences, i.e. before Pal2Nal. The reality I can probably solve this with all the information. At present I can make a guess, but it's no better than a guess. | |
| Jun 26, 2023 at 2:29 | comment | added | Sudoh | The peptides are equal in length once they are aligned alongside their orthologs/homologs (i.e. on the other side of sequence alignment). With MAFFT the peptides become something like 31k (including gaps) characters long. Post translation the sequences are something like 93k long and the ones out of whack are about 54k (all of them, the same exact length). Sorry for the confusion, the peptides are not supposed to be the same length per-alignment. | |
| Jun 25, 2023 at 23:22 | comment | added | M__♦ | The example looks fine to me. The peptide causing an issue is 69 residues in length and the cds is 207, which is correct. If the peptide is supposed to be ~140 residues we'd need to see the full length peptide and/or nucleotide. BTW what is the proportion of half lengths against full transcripts? | |
| Jun 25, 2023 at 23:08 | history | asked | Sudoh | CC BY-SA 4.0 |