Link to this post | posted 21 Jan, 2022 20:05
cdherren	Got it!

Link to this post | posted 21 Jan, 2022 14:21
cdherren	So it's this one? 164Kb

Link to this post | posted 20 Jan, 2022 21:39
cdherren	This is from DNA Master Update – Restores Genemark/Glimmer Functionality (9/14/17) 207Kb

Link to this post | posted 20 Jan, 2022 21:38
cdherren	This is from the online manual 164Kb

Link to this post | posted 20 Jan, 2022 19:17
cdherren	Are the best Gene Prediction addresses the FTP addresses in the online annotation guide or the opal.gatech and ncbi addresses?

Link to this post | posted 20 Jan, 2022 18:39

cdherren

I got it to work. In the forums there is the older post for having 4 secure connections and then there's the DNA Master Update – Restores Genemark/Glimmer Functionality (9/14/17) that goes to 2 secure connections and changes the prediction settings. I merged the DNA Master Update – Restores Genemark/Glimmer Functionality (9/14/17) with the original DNA Master Installation Guide for a DNA Master Installation Guide (1.20.22) 179Kb

Link to this post | posted 19 Jan, 2022 01:04

cdherren

My version 5.32.6 build 2705, running as administrator, will update the database, but won't auto-annotate. It only says, "Annotation error". The log says it did everything, but there are no features and it opens an excel table with only headers and no data entries: Auto-annotation of Extracted from FastA Library Halo3.fasta begun at 6:59:44 PM Predicting genes at 6:59:44 PM Predicting tRNAs at 6:59:46 PM Parsing genes at 6:59:48 PM Learning genes at 6:59:48 PM Skipping BLAST at 6:59:49 PM Doing Profile at 6:59:49 PM Performing Frames Analysis at 6:59:50 PM Skipping Start Codon Analysis at 6:59:51 PM Performing Gray Holes Analysis at 6:59:51 PM Creating GC-Content Plot at 6:59:51 PM Auto-annotation Complete at 7:00:30 PM 2Kb

Link to this post | posted 27 Jan, 2021 20:17
cdherren	Makes complete sense! Thanks

Link to this post | posted 27 Jan, 2021 19:10

cdherren

The Phamerator explanation sounds right and I probably should have remembered that, but isn’t DNA Master & PECAAN doing BLASTx searches? https://blast.ncbi.nlm.nih.gov/Blast.cgi I was taught BLASTx takes a nucleotide sequence, virtually translates it to the 1 possible amino acid sequence and then searches protein databases. BLASTp compares amino acids sequences to protein databases, where the amino acids are usually derived from mass spectrophotometry of a purified protein. BLASTn takes a nucleotide sequence, derived from DNA sequence analysis, and compares it to nucleotide databases. Finally, tBLASTn is the reverse of BLASTx, it takes an amino acid sequence, again usually derived from mass spectrophotometry of a purified protein, virtually derives all possible nucleotide sequences accounting for codon redundancy and compares all of them against nucleotide databases. BLASTx and BLASTp both compare to protein databases, but the previous inputs DNA sequence and the later inputs amino acid sequence. Even if DNA Master and others are doing the virtual translation and not the BLAST website, aren’t those technically still BLASTx searches since the input is DNA sequence and the output is protein hits?

Link to this post | posted 26 Jan, 2021 01:54
cdherren	Are DNA Master and Phamerator using BLASTx (DNA > protein) for "Blast" searches? The input is DNA but the results show amino acid alignments & scores. How about PECAAN? What it calls 'Phagesdb BLAST' and 'NCBI BLAST' look to be reporting in amino acid lengths, not base pair lengths.