How to generate Protein Table file ( .ptt ) and RNA table file ( .rnt ) from a nucleotide fasta file?

Question

[Optimist]

Hello Biostar community

I need your help and inputs in generating Protein Table file ( .ptt ) and RNA table file ( .rnt ) from an assembled bacterial genome.

I have Fasta & genbank files of the same. Are there any tools that can generate .ptt & .rnt files using my .fna file as input.

Any advice or suggestions in this direction is appreciated.

Thanks & regards

Optimist

[Sej Modha]

What have you tried so far?

Did you look at previous threads discussing this? e.g. Problem combining ptt, rnt files How do I make a .rnt file for EDGE-pro. What is it, and can it be made from a .gbk file?

Have you tried any existing scripts available to do this? e.g. https://github.com/ajvilleg/gbk2ptt

Can you post sample accession numbers for which you have already got .gb file?

[Optimist]

Hello Sej Modha,

Thanks for the links you've provided. I'll read-up the protocols. I'm working on bacterial genome Pseudomonas aeruginosa PAO1. details regarding the assembly is added below for your perusal.

RefSeq - NC_002516.2
INSDC - AE004091.2
Size (Mb) - 6.26
GC% - 66.6

Thanks & Regards

Optimist

Answer 1

[Sej Modha]

I have tried https://raw.githubusercontent.com/ajvilleg/gbk2ptt/master/GBKtoPTT.pl with NC_002516.2 and it can generate a properly formatted .ppt file. Here are a few lines from the output.ptt file.

Pseudomonas aeruginosa PAO1 chromosome, complete genome. - 0..6264404
5572 proteins
Location    Strand  Length  PID Gene    Synonym Code    COG Product
483..2027   +   514 -   dnaA    PA0001  -   chromosome replication initiator DnaA
2056..3159  +   367 -   dnaN    PA0002  -   DNA polymerase III subunit beta
3169..4278  +   369 -   recF    PA0003  -   DNA replication and repair protein RecF
4275..6695  +   806 -   gyrB    PA0004  -   DNA gyrase subunit B
7018..7791  -   257 -   lptA    PA0005  -   lysophosphatidic acid acyltransferase
7803..8339  -   178 -   -   PA0006  -   D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase
8671..10377 +   568 -   -   PA0007  -   hypothetical protein

[Optimist]

Thank You for the quick revert.

I'll follow the link you have provided.

Regards

Optimist