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

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

blast
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updated by Ram Ram • written by Arun • Arun

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....

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written by Torst Torst

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.

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written by Mel161803 • Mel161803

3 answers

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!

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written by Steve Moss Steve Moss

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

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written by a.a.kechin • a.a.kechin

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

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updated by Ram Ram • written by arniie.me • arniie.me

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

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written by matteo.ferla • matteo.ferla

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.

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written by Mel161803 • Mel161803

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