genoma.unsam.edu.ar :: BLAST :: databases

Databases available at our BLAST server

Notice to external users: some of the databases included in our BLAST service are only available for internal use. Sorry.

Nota para usuarios del IIB: se escuchan sugerencias sobre agregados de otras bases de datos que les sean de utilidad.


Trypanosomatid databases

Trypanosoma cruzi GSSs

[See project stats]
Random genomic sequences from Trypanosoma cruzi CL Brener strain. All ~12000 sequences have been produced at IIB-UNSAM and are also deposited in the GSS division of GenBank (gbdiv gss). This dataset contains quality clipped, vector masked sequences that are longer than 100 bp.

Trypanosoma cruzi epimastigote ESTs

Random cDNA sequences from Trypanosoma cruzi CL Brener culture epimastigotes. All ~10000 sequences are derived from a normalized cDNA library (J Eukaryot Microbiol 46 (1999): 542-4). Sequencing was done at Uppsala University (Sweden), IIB-UNSAM (Argentina), Instituto Fiocruz (RJ, Brasil) and Instituto de Parasitologia (Granada, España). The library is oriented and sequencing was done from the 5' end.

Trypanosoma carassii trypomastigote ESTs

[See project stats]
Random cDNA sequences from Trypanosoma carassii blood trypomastigotes. Total RNA from T. carassii trypomastigotes was provided by Dr. Peter Overath (Max-Planck Institut, Germany). Sequences are derived from an oriented cDNA library constructed by Vanina Campo in Dr. Frasch's lab at IIB-UNSAM. The library is oriented and sequencing was done from the 5' end.

Trypanosoma cruzi trypomastigote ESTs

[See project stats]
Random cDNA sequences from Trypanosoma cruzi CL Brener culture trypomastigotes. The trypomastigote library was produced by Dr. Antonio Gonzalez (Universidad de Sevilla, España). Since trypomastigotes are produced by infection of human culture cells, there could be contaminant human sequences in the dataset. Preliminar analyses showed 0.33% of contamination with ALU sequences. These have been removed from the dataset, but other contaminating sequences might remain. Caveat emptor.

Trypanosoma cruzi amastigote ESTs

[See project stats]
Random cDNA sequences from Trypanosoma cruzi CL Brener culture amastigotes. Second cDNA strand was synthesized using a SL primer, and ESTs were sequenced from the SL end (SL = spliced leader).The amastigote library was produced and sequenced by Dr. Antonio Gonzalez (Instituto de Parasitología y Medicina, Granada, España).

Trypanosoma cruzi subtracted trypomastigote ESTs (IIB-UNSAM)

[See project stats]
Random cDNA sequences from a trypomastigote subtracted library. This is an ongoing project, thus the dataset will keep growing in the following months (we're in April 2002 as of this writing). Trypomastigote RNA is subtracted with epimastigote RNA. Preliminary analysis of these sequences to search for contamination has not been performed. Caveat emptor.

Trypanosomatid ESTs (GenBank)

This dataset includes all Kinetoplastid ESTs currently available from GenBank (it does not include finished mRNAs which are not usually in the GenBank EST division). They are automatically retrieved using Entrez (see query below).This dataset contains sequences from some of the EST datasets mentioned in this page.

Entrez query: Kinetoplastida[ORGN] AND "gbdiv est"[PROP]

[Notice] This dataset is built from GenBank data. Searching the corresponding GenBank divisions at other sites should provide similar results. This dataset is provided here as a service, and may be discontinued if the load on our server gets beyond a reasonable limit.

Trypanosomatid GSSs, HTG and finished sequences.

This dataset includes all Kinetoplastid genomic sequences available from the GSS and HTG (High Throughput Sequencing) GenBank divisions together with finished chromosome sequences. They are automatically retrieved using Entrez (see query below).This dataset contains sequences from some of the GSS datasets mentioned in this page.

Entrez queries: Kinetoplastida[ORGN] AND ("gbdiv gss"[PROP] OR "gbdiv htg"[PROP])

[Notice] This dataset is built from GenBank data. Searching the corresponding GenBank divisions at other sites should provide similar results. This dataset is provided here as a service, and may be discontinued if the load on our server gets beyond a reasonable limit.


Bacterial databases

Brucella abortus GSSs

[See project stats]
Random genomic sequences from Brucella abortus 2308. The sequences are derived from three different genomic libraries: one M13 library was used to produce ~600 random sequences at Uppsala University (Dr. Siv Andersson) and two plasmid libraries were sequenced at INTA and IIB-UNSAM, respectively. The sequences in this dataset can be also obtained from public databases (GenBank).

Campylobacter fetus genome project

[See project stats]
This dataset contains unfinished sequences from the C. fetus genome project. Currently this means unassembled reads and contigs and singletons derived from automatic unsupervised assembly of the shotgun reads.

alpha-proteobacteria sequences

This is a sequence dataset built from sequences present in GenBank using a customized Entrez query (see below). It consists of all genomic sequences from members of the alpha-proteobacteria group. It may contain both finished or unfinished sequences.

Entrez query: a-proteobacteria[ORGN]

[Notice] This dataset is built from GenBank data. Searching the corresponding GenBank divisions at other sites should provide similar results. This dataset is provided here as a service, and may be discontinued if the load on our server gets beyond a reasonable limit.


Other databases

Tupaia belangeri subtracted hippocampus ESTs

This dataset contains randomly sequenced cDNA ends from two different subtracted libraries from T. belangeri (tree shrew) hippocampus.