Version 2015

"velut arbor aevo"

- As a tree with the passage of time

Version 2015 - Baltra Island

Oxford Journals: Database - Pre_GI

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Bacterial / archaeal replicons analyzed ( 2,407 )
Predicted genomic islands ( 26,744 )
Last update ( 28 February 2017 )
Taxonomy Statistics

About This Project

"in scientia opportunitas"

- In Knowledge, there is Opportunity

Pre_GI database is a web-based database which forms part of the SeqWord Project. This dynamic database aids in genomic island research and is frequently updated to ensure the inclusion of significant and novel data with users able to browse present genomic islands or search and compare with their own genomic islands. The driving force behind the creation of the Pre_GI database was the development of a web-based analytical resource to deconstruct the ontological relationships between bacterial / archaeal mobile genetic elements and reconstruct the global fluxes of genetic vectors through taxonomic barriers. Bearing this in mind the Pre_GI database interface includes various diagnostic tools for the comparison of newly identified and presently residing genomic islands and the reconstruction of possible donor-recipient movements between species.

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GI prediction

"disce quasi semper victurus vive quasi cras moriturus"

- Learn as if always going to live; live as if tomorrow going to die

Pre_GI database houses genomic islands predicted by the SeqWord Genomic Island Sniffer program using oligonucleotide signatures of the genomic fragments.

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How to use

"ipsa scientia potestas est"

- knowledge itself is power

Browse Pre_GI Database may be used to browse currently residing genomic islands. The hyperlink will display a list of current analyzed bacterial / archaeal sources. The list can be scrolled down to find a source or the source accession and source description fields may be used to aid the search. Each accession number is hyperlinked to display all predicted genomic islands for the source. Genomic islands may be inspected by the hyperlink on the genomic island start location.

Cluster representatives contains 420 cluster / sub cluster genomic island representatives used to facilitate updates and aid in novel genomic island comparisons to the database. The hyperlink will display all representatives and cluster / sub cluster that they represent.

Browse by gene annotation may be used to browse against the database with the aid of gene annotations. This will identify similar gene annotations in the database and the genomic islands they occur in.

Search by location may be used to search against the database with the aid of source accession and genomic island locational start and stop. This will identify any overlaps with the database.

BLASTN will identify hits with a novel query nucleotide sequence against the database. This hyperlink will enable sequence similarity comparisons to the database.

Compositional similarity utilize oligonucleotide usage patterns, 4-mers, to compare compositional similarity. Novel genomic island nucleotide sequences may be entered to identify hits above 75% similarity.

Upload for analysis allows for up to 8 seqword genomic island sniffer generated genomic island genbank files to be uploaded. This application performs all comparisons against the database concurrently.

Taxonomy Statistics provides general statistics on the taxonomical distribution of the database.

Download SWGIS to get a copy of the standalone island identifier program.

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