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Table 2 Availability of GeneViTo input data.

From: GeneViTo: Visualizing gene-product functional and structural features in genomic datasets

Online Resources

Type of Data

Essential

URL

GenBank

Protein Table

yes

ftp://ftp.ncbi.nih.gov/genbank/genomes/

 

FASTA nucleotide coding regions file

yes

ftp://ftp.ncbi.nih.gov/genbank/genomes/

 

FASTA Nucleic Acid file

yes

ftp://ftp.ncbi.nih.gov/genbank/genomes/

 

Cluster of Orthologous Groups (COGs)

no

http://www.ncbi.nlm.nih.gov/COG/

 

Translation table

no

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c

Proteome Analysis Server (EBI)

Complete Proteome

yes

http://www.ebi.ac.uk/proteome/index.html

SwissProt

  

http://us.expasy.org/sprot/

WebCutter

Restriction Enzymes Sites

no

http://www.firstmarket.com/cutter/cut2.html

PRED-CLASS

Protein Structural Classification

no

http://biophysics.biol.uoa.gr/PRED-CLASS/

PRED-TMR2 and orienTM *

Prediction of TM region location and orientation

no

http://biophysics.biol.uoa.gr/PRED-TMR2/, and http://biophysics.biol.uoa.gr/orienTM/

SIGNALP

Signal Peptides

no

http://www.cbs.dtu.dk/services/SignalP/

  1. A list of web-based resources and tools providing input data for visualization with GeneViTo. Essential data types are the minimum required data-set in order to load a Genome into GeneViTo. * PRED-TMR2 and orienTM can be executed in a single step from the orienTM web-server http://biophysics.biol.uoa.gr/orienTM/