Release VB-2014-08

Overview

We are pleased to announce the August release of VectorBase (VB-2014-08):

• Minor gene prediction modifications for 16 species to capture missing stop codons
• The expression browser has been updated and is now ready to incorporate RNA-Seq differential expression data.
• A new variation database for Anopheles stephensi SDA-500 strain.
• Galaxy is upgraded to Beta version. The available computing resources have been extended to meet user requirements.
• Advanced Search has been improved. Users can now bookmark the Advanced Search URLs.
• BLAST, ClustalW, and HMMER job expiration will be enforced; Jobs ran while not logged in will expire after 14 days, jobs ran while logged in will expire after 90 days. Jobs saved under the user profile page will be saved indefinitely until the user chooses to not save them anymore.
• BLAST default datasets and options may be saved while logged in.

Genomes

VectorBase is committed to a new release every two months with all data freely available for public use based on NIH/NIAID policy. A list of these changes and the state of current versions on this date (e.g., current gene sets) can be found on the Releases section of VectorBase.

For your species of interest, click on Organism, Strain, Assembly, or Gene set to find the Genome Browser link (which looks like this:  ).

Released genomes, with gene predictions

Organism	Strain	Assembly	Gene set	Gene Count	Browser
Aedes aegypti	Liverpool	AaegL3	AaegL3.2	17 479
Anopheles albimanus	STECLA	AalbS1	AalbS1.2	12 335
Anopheles arabiensis	Dongola	AaraD1	AaraD1.2	13 678
Anopheles atroparvus	EBRO	AatrE1	AatrE1.2	14 230
Anopheles christyi	ACHKN1017	AchrA1	AchrA1.2	11 156
Anopheles culicifacies A	A-37	AculA1	AculA1.2	14 882
Anopheles darlingi	Coari	AdarC3	AdarC3.2	10 948
Anopheles dirus A	WRAIR2	AdirW1	AdirW1.2	13 239
Anopheles epiroticus	Epiroticus2	AepiE1	AepiE1.2	12 602
Anopheles farauti	FAR1	AfarF1	AfarF1.2	13 703
Anopheles funestus	FUMOZ	AfunF1	AfunF1.2	13 756
Anopheles gambiae	PEST	AgamP4	AgamP4.2	13 624
Anopheles maculatus B	maculatus3	AmacM1	AmacM1.2	15 046
Anopheles melas	CM1001059	AmelC1	AmelC1.2	16 666
Anopheles merus	MAF	AmerM1	AmerM1.2	14 415
Anopheles minimus A	MINIMUS1	AminM1	AminM1.2	13 128
Anopheles quadriannulatus A	SANGWE	AquaS1	AquaS1.2	13 857
Anopheles sinensis	SINENSIS	AsinS1	AsinS1.2	15 280
Anopheles stephensi	Indian	AsteI2	AsteI2.2	12 350
Anopheles stephensi	SDA-500	AsteS1	AsteS1.2	13 650
Culex quinquefasciatus	Johannesburg	CpipJ2	CpipJ2.2	19 363
Glossina morsitans	Yale	GmorY1	GmorY1.4	12 963
Ixodes scapularis	Wikel	IscaW1	IscaW1.4	20 771
Musca domestica	Aabys	MdomA1	MdomA1.1	15 803
Pediculus humanus	USDA	PhumU2	PhumU2.1	11 699
Rhodnius prolixus	CDC	RproC1	RproC1.2	17 244

Pre-released genomes, with mapped data but no gene predictions

Organism	Strain	Assembly	Gene set	Gene Count	Browser
Anopheles coluzzii	Mali-NIH	AcolM1	AcolM1.1	14 703
Biomphalaria glabrata	BB02	BglaB1	BglaB1.2	14 351
Lutzomyia longipalpis	Jacobina	LlonJ1	LlonJ1.1	10 429
Phlebotomus papatasi	Israel	PpapI1	PpapI1.1	12 678

Genome annotation

• Gene predictions have been extended to find plausible stop codons (where absent) which are proximal to the end of the transcript predictions. In total 16 species have been updated:
  • Aedes aegypti AaegL3.2
  • Anopheles albimanus AalbS1.2
  • Anopheles arabiensis AaraD1.2
  • Anopheles christyi AchrA1.2
  • Anopheles darlingi AdarC3.2
  • Anopheles dirus AdirW1.2
  • Anopheles epiroticus AepiE1.2
  • Anopheles funestus AfunF1.2
  • Anopheles gambiae AgamP4.2
  • Anopheles minimus AminM1.2
  • Anopheles quadriannulatus AquaS1.2
  • Anopheles stephensi AsinS1.2
  • Biomphalaria glabrata BglaB1.2
  • Culex quinquefasciatus CpipJ2.2
  • Glossina morsitans GmorY1.4
  • Ixodes scapularis IscaW1.4

Expression Data

One new experiment has been added:

• Blood fed vs. Sugar Fed (Bonizzoni et al., 2011) (Aedes aegypti)

Several improvements have been made to the expression browser pages:

• RNA-Seq experiments with biological replicates can now be incorporated into the resource. One RNA-Seq experiment for Aedes aegypti (see above) has been loaded to demonstrate this new functionality.
• A problem with the CSV-format table downloads has been fixed, and are also more spreadsheet-friendly.
• Probes are called probes (or probe sets or reference transcripts) and the terminology "reporter" has been phased out.
• Now hosted on the main server farm for improved robustness and consistency.

Population Biology/Insecticide Resistance

A large batch of insecticide resistance studies has been imported from IRBase, bring the total number of projects in the population biology browser to 99.

Variation Data

New data

A new variation database has been added for the Anopheles stephensi SDA-500 strain.

Updates

Variation transcript effects were re-evaluated this release for all species.

Summary of available variation data by organism

Mitochondrial gene summaries for VectorBase genera

Links to Mitochondrial data for the 4 main genera are presented below for convenience.

Ontologies

Tutorials

Follow this link for the tutorials page, which also includes videos, practice exercises, and sample files.

Known issues

• The new RNA-Seq expression data appears to be missing from the expression BioMart - we will fix this before the next release if possible.

Please report any problems to the helpdesk.