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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.
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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
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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.
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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 |
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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 |
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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.
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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)
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© 2009, Institute for Systems Biology, All Rights Reserved
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