Closed dcraheem closed 4 years ago
seed doesn't matter, can use a mouse sequence for human, still works length doesn't matter as long not shorter than the read length, probably will only use the first 100 to 200 bp anyway
Do you mean that novoplasty probably uses only the first 100-200bp of the seed sequence?
Yes, unless it doesn't finds a match there, it will continue further
Thanks very much for the advice and the software.
The mt genomes I am assembling using novoplasty represent several species in a single land-snail genus. I have previously assembled and annotated complete mt genomes for other species in this same genus.
1) Would the sequence of a highly-conserved gene (e.g. cox1, cox2 or cox3) from one of these previously assembled genomes make a suitable seed for my novoplasty assembly?
2) If I use a gene like cox1, should the sequence of the whole gene be used? For my genus, the total length of the cox 1 gene is c. 1600 bp (700-800 bp for the cox 2 and cox 3 genes).