Integrated Proteogenomics Database

iPtgxDB combiner settings

iPtgxDB combiner merges annotations from different sources, including reference genome annotation(s), ab initio prediction(s) and our in silico annotation (all in GFF format). Protein coding sequences (CDS) from all annotation sources are consolidated into protein annotation clusters (shared stop codon). The annotations are merged hierarchically (thus, the order in which you enter annotations matters!), whereby identical sequences are collapsed and unique and information-rich iPtgxDB identifiers are generated that are incorporated in the output FASTA database. The output is

a minimally redundant, searchable iPtgxDB protein database (fasta format),
the combined annotations (gff format), that can be loaded in a genome browser like IGV, and
a detailed matching table (tsv format).

Taxonomy

Organism taxonomic name*

Can be either in the binomial or trinomial form

Strain name

Sequence

Genome sequence file*

Source sequence file, in FASTA format

Gene identifier prefix*

Parameters

Ignore pseudogene entries If checked, pseudogene entries will not be read from the annotation files

Protease*

Genetic code*

Reference annotations

Annotation hierarchy

The generation of iPtgxDBs strictly follows a hierarchical annotation (see the pyramid in Fig. 3A). Highest preference is given to reference genome annotations (RefSeq, Ensembl, Genoscope, JGI or any other annotation source that is derived from a reference database) to leverage the quality of manual curation efforts, followed by ab initio predictions and then our in silico annotation. Therefore, these annotations are arranged serially in the entry form. It is critical that the annotation options and the corresponding GFF files (whichever available) are uploaded in this precise order. We recommend the users to provide at least one Reference annotation when trying to create an iPtgxDB for a key model organism (see the blue containers in the top row of Fig. 1).

This

sample
                            file

shows an example on how we run iPtgxDB combiner for the prokaryotic genome Bartonella henselae which will give you an idea on how you could best order the annotation sources for your genome.

Converted annotation file

Annotation*

Annotation file, in GFF format

Source*

Label

Used as tag in the iPtgxDB

Ab initio annotations

Annotation hierarchy

Please note the comment above.
We highly recommend the users to rely on Prodigal for an ab initio annotation and include it when creating an iPtgxDB for a newly sequenced genome or de novo assembly without existing reference annotations.

Genome annotation derived from one or more ab initio algorithms (e.g. Prodigal, Chemgenome, Glimmer or GeneMark, etc.).

Converted annotation file

Annotation*

Annotation file, in GFF format

Source*

Label

Used as tag in the iPtgxDB

In silico annotations

Generates a GFF file of all possible ORFs for the provided genomic sequence, thus including potential correct short ORFs that might have been missed in the reference and ab initio genome annotations. In contrast to a standard six frame database translation, our approach scans the genome sequence in all six frames for the longest possible ATG-initiated ORFs. Extensions are only considered for the alternative start codons TTG, GTG, and CTG. Overall, we select for ORFs longer than 18 aa (our recommendation).

On-the-fly
Pre-computed with iPtgxDB_insilico.jar

Alternative start codons*

Longest alternative anchor only For regions without a main start codon, take only the longest alternative anchor

Minimal protein length*

Minimum protein length in aa for export in protein database

Genetic code*

Annotation*

Annotation file, in GFF format

Alternative start codons*

Longest alternative anchor only For regions without a main start codon, take only the longest alternative anchor

Minimal protein length*

Minimum protein length in aa for export in protein database

Genetic code*

Submit Job

Submitting the job will forward you to the job overview, where you can monitor the progress of your job.

Do it yourself!

iPtgxDB combiner settings

Reference annotations

Annotation hierarchy

Ab initio annotations

Annotation hierarchy

In silico annotations

Submit Job