What Is A .Ptt File And How It Is Created?

Question

[Arun]

what is a .ptt file and how it is created?

[Aaronquinlan]

Googling ".ptt file" yields: http://doc.bioperl.org/bioperl-live/Bio/FeatureIO/ptt.html

[Torst]

Yes, I wrote that module. There are still some tools that want a PTT file. They aren't much use for unfinished genomes, because they can only refer to ONE sequence at a time, so if you have 200 contigs, you need 200 PTT files....

[Mel161803]

I was just having this problem, and ended up using the perl script I got from here. gb2ptt Just note that you should run the script as "perl gb2ptt.pl --infile filename.gbk" instead of what they said.

Answer 1

[Steve Moss]

A .ptt file is an NCBI Protein Table file, which is a tab delimited file containing a list of all the proteins for their genomes (ftp://ftp.ncbi.nih.gov/genomes/). It corresponds with the CDS annotations from the GenBank file and can be created by parsing the GenBank files and writing the appropriate output.

The columns are:

Location    Strand    Length    PID    Gene    Synonym    Code    COG    Product

For example ftp://ftp.ncbi.nih.gov/genomes/Fungi/Aspergillus_niger_CBS_513_88_uid19263/NC_007445.ptt. These correspond to the feature start and end coordinates, the strand (+/-), the length of the amino acid (minus stop codon), and items analogous to various other GenBank format fields.

You can use BioPerl, as aaron suggests, but it appears as though the BioPython functionality has been dropped? It shouldn't be hard to write your own parser to be honest, although it doesn't store any sequence information!

Answer 2

[a.a.kechin]

I've found useful and simple tool for this purpose https://lfz.corefacility.ca/gbk2ptt/

[arniie.me]

Using https://lfz.corefacility.ca/gbk2ptt/ I converted a gbk file to .ptt .......which gave a result of

Legionella pneumophila subsp. pneumophila str. Philadelphia 1 chromosome, complete genome. - 0..3397754
2021 proteins

While later in NCBI I got

Legionella pneumophila subsp. pneumophila str. Philadelphia 1 chromosome, complete genome - 1..3397754
2943 proteins

Can you explain

[matteo.ferla]

The tool seems to parse the first record, but discards the rest.

[anabio86]

This link is not working.

Answer 3

[Mel161803]

https://github.com/sgivan/gb2ptt/blob/master/README.md

Just note that you should run the script as "perl gb2ptt.pl --infile filename.gbk" instead of what they said.

[rohitsatyam102]

Or you can use this one: https://github.com/ajvilleg/gbk2ptt