Tools

As a step towards the development of a useful working environment, ParameciumDB provides some bioinformatics services.

BioMart advanced query interface

The BioMart interface allows you to "mine" the genomic data in ParameciumDB using multi-criteria searches.

Blast

ParameciumDB blast server. You can currently blast against the macronuclear genome assembly, against the proteins predicted by Genoscope's automated annotation, reads, etc...

Align two nucleotide sequences

The link (i.e. the title of the paragraph) takes you to a form that will allow you to enter two sequences, by pasting them, by providing Gene IDs or by specifying their positions and orientations on the scaffolds. The EMBOSS package Smith-Waterman alignment program will align the two sequences, and we have added a histogram and colored the alignment to show the size and positions of stretches of identical nucleotides. This tool is useful for designing and interpreting RNA interference experiments.

Blat server at Genoscope

This link takes you to Genoscope's Paramecium Blat server.

Get nucleotide sequence

With the position in the genome, you can get the nucleotide sequence.