Question: What Is A .Ptt File And How It Is Created?
0
gravatar for Arun
7.9 years ago by
Arun0
KOLKATA
Arun0 wrote:

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

blast • 17k views
ADD COMMENTlink modified 11 months ago by Mel1618030 • written 7.9 years ago by Arun0
4

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

ADD REPLYlink modified 19 months ago by h.mon28k • written 7.9 years ago by Aaronquinlan11k
2

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....

ADD REPLYlink written 5.4 years ago by Torst950

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.

ADD REPLYlink written 14 months ago by Mel1618030
5
gravatar for Steve Moss
7.9 years ago by
Steve Moss2.3k
United Kingdom
Steve Moss2.3k wrote:

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!

ADD COMMENTlink written 7.9 years ago by Steve Moss2.3k
1
gravatar for a.a.kechin
4.9 years ago by
a.a.kechin20
Russian Federation
a.a.kechin20 wrote:

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

ADD COMMENTlink written 4.9 years ago by a.a.kechin20

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 
ADD REPLYlink written 4.7 years ago by arniie.me0

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

ADD REPLYlink written 4.3 years ago by matteo.ferla0

This link is not working.

ADD REPLYlink written 13 months ago by anabio860
0
gravatar for Mel161803
11 months ago by
Mel1618030
Sydney
Mel1618030 wrote:

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.

ADD COMMENTlink written 11 months ago by Mel1618030
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