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hyattpd / Prodigal

Prodigal Gene Prediction Software
GNU General Public License v3.0
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can prodigal predict metatranscriptome? #68

Open ucassee opened 4 years ago

ucassee commented 4 years ago

Hi, I use Spades to assemble my metatranscriptome. I wonder whether prodigal can predict protein from assembled metatranscriptome?

hyattpd commented 4 years ago

This should work on bacterial/archaeal/viral transcripts ok.

There might be some cases where it predicts a partial gene at the beginning of a fully assembled transcript (because it thinks this is genomic DNA), especially if that gene is leaderless.

ucassee commented 4 years ago

Hi @hyattpd ，assembled metatranscriptome is gDNA. But I wonder if the transcripts are incomplete, such as missing the promoter or terminator, can prodigal predict these incomplete transcripts?

tseemann commented 4 years ago

The transcripts will most certainly be incomplete, especially if it is a meta-transcriptome. How many "transcripts" did you get, and what was the length distribution?

ucassee commented 4 years ago

The following is the length statistics of my assembled transcripts: N90 304 545605 N80 368 425143 N70 446 325729 N60 543 243890 N50 660 176613 N40 802 121254 N30 983 75831 N20 1249 39280 N10 1846 11974 Max length 385529 Total length 402020685 Total number 694775 Average length 578 Number>500bp 275715 Number>1000bp 72491 Number>2000bp 9488 Number>5000bp 656 Number>10kbp 157