PeptideAtlas builds are available for download as a group of
three different file formats,
each containing some unique information not found in the
other file formats.
FASTA format file: A file of sequences from the PeptideAtlas
build where the first line is ">" followed by the PeptideAtlas accession
and the second line is the peptide amino-acid sequence.
>PAp0000001 AAHEEICTTNEGVMYR
Biosequence Set: the FASTA file that we map the peptide sequences to. It includes
the database (including decoys) we use to do the searches, and may includes the ensemble
database if available.
CDS coordinates file:
A file containing the peptide accession, and the position of the peptide
relative to protein start (CDS coordinates).
PeptideAtlas accession
Sequence length
Protein accession
Length of sequence match
% Identity (=% match of sequence)
Start of sequence in protein CDS
End of sequence in protein CDS
Difference between sequence and matched sequence
PAp00000135
10
ENSP00000315757
10
100
40
49
0
CDS and Chromosomal Coordinates file:
A file containing the peptide accession, the peptide's position within a protein
relative to protein start (CDS coordinates), and it's chromosomal coordinates.
PeptideAtlas accession
Sequence length
Protein accession
Length of sequence match
% Identity (=% match of sequence)
Start of sequence in protein CDS
End of sequence in protein CDS
Difference between sequence and matched sequence
Protein description
Strand
Start of sequence in chromosome
End of sequence in chromosome
Transcript ID
Gene ID
PAp00000135
10
ENSP00000315757
10
100
40
49
0
chromosome:NCBI35:13:1:114142980:1
-1
45631043
45631072
ENST00000323076
ENSG00000136167
Database export XML:
This file contains the contents of the various tables in the Peptide Atlas
schema for a specified build, exported in an XML format. This format is
suitable for loading into a preexisting PeptideAtlas schema using the SBEAMS
DataImport.pl script. This format can be loaded into mysql or MS SQL Server
databases, and could possibly be used for others.
mysqldump export file:
Peptide Atlas schema and data for a given build exported using mysqldump
utility. The data can be loaded into an empty mysql instance with the
mysql command-line utility as follows:
mysql -u username -D database < PA_export.mysql
This greatly accelerates loading the data info a mysql instance
relative to the xml format above, but would probably require some changes
to work with a database other than mysql (SQL dialect issues)
