HowTo ProtozoaDB

ProtozoaDB is a warehouse designed to search DNA, RNA and protein sequences from 5 protozoan genomes: Trypanosoma cruzi, T. brucei, Leishmania major, Plasmodium falciparum and Entamoeba histolytica. It is based on the Genomics Unified Schema (GUS) and offers a modern Web-based interface for user-friendly data visualization and exploration.

To start, in ProtozoaDB you may choose to Search sequences or Phylogenetics.

In Search sequences option you may choose search genes for all species or each protozoa separately. by genes ID number, keyword and sequence type or protein motif .

In Search genes by ID: eg: AAC77873.1, results shows information related with gene Id, name (CDS: coding sequences, or mRNA, rRNA, tRNA, snRNA, snoRNA, primary transcript, precursor RNA or untranslated sequence), product, description and organism.

Moreover, information related with sequences features, sequences DNA and protein of the query may be obtained in

In Search sequences by Keyword and sequence type

you can choose keyword, eg: tubulin or sequence type, and select one organism or all in Genbank and/or RefSeq databases.

Information related with gene Id, Name, Product and description of gene are showed. Moreover information about sequences like above may be obtained.

In Search genes by protein motif: eg: NMNDLVS, you can search proteins with a specific motif

Here, you can obtained information related with Id, name, product and description of the protein containing the motif

Additionally, ProtozoaDB allows to make the search for each organism separately, in the same way like Search Sequences for all organisms. Eg.: Entamoeba histolytica.You can find information related with the organism

Also, Search EST in libraries and strains specific for each one of them.

Phylogenetics

Phylo Schema was designed to store information related and generated from phylogenetic analysis, bioinformatics software tools and resources available. PhyloSearch integrates a wide array of biological data, informatics methods, bioinformatics software tools and resources available of Phylogenetic Analysis organized on the basis of structural similarity and by evolutionary information. PhyloSearch is motivated by two of the biggest lessons of the post-genome era - the power of integrating phylogenetic data, for example multiple sequence alignment, consistent evolutionary models and phylogenetic matrix and trees; and inference tools from different sources, improved prediction accuracy using consensus approaches in bioinformatics.

To start, in Phylogenetics click PhyloSearch.

In PhyloSearch option you may choose Search Phylogenetics for Studies, Analyses or Trees.

In Search Phylogenetic Studies, you can do the request by Keyword or information about the Author (1st name, Last name and email).
In Search Phylogenetic Analysis, by Description (genes or sequence types) or Name assigned to the Analysis.
In Search Phylogenetic Trees, by Name and Type of the trees or Species (taxon).

In Phylogenetic Studies, by keyword, eg: MGE, you can obtain information related to Study, Analysis Name and Analysis Description, about all the studies containing MGE, used as keyword.
Moreover, information about the Analysis of the query (MGE-AA-RH) can be obtained in

Here is the information related to the Analysis Study: Analysis Name, Tree Name, Tree Type and Tree Quality.
More information about the Tree of the query (MGE-AA-RH) can be obtained in

Here is the information related to the Tree Analysis Study. They are divided in Tree Organisms and Tree Features.

Tree Organisms, shows Taxon Id, Taxon Name and Taxon Weight related to the tree in study.
Tree Features, shows some parameters and features with the respective values, also related to the tree, as mentionated above.

Finally, for access to the phylogenetic phylogram click on button 'Click to view Tree'

Phylogenetic Tree Construction and Visualization: Neighbor-Joining trees are constructed with PAUP software, using the default parameters for 'Mafft', 'modelgenerator' and 'neighbor' (JTT model and no variation of rates). All trees are rooted and bootstrapped with 1 000 repetitions. Neighbor-Joining trees include branch lenghts values for every nodes and will eventually include bootstrap values, for the consensus majority-rule phylogenetic tree.

Future work

In future releases, we plan to include Maximum Likelihood, Maximum Parsimony and Bayesian Inference analyses.
Users will be able to navigate between steps in the same pathway using the stored information or suggest other types, eg. carrying on external data.
Users will be able to retrieve evolutionary models for proteins or nucleotides through hyperlinks on modeltest, protest, or modelgenerator pages. We plan to reduce the computational cost on searches by combining information between the different steps, that could be taken as initial point.
We will also include novels phylogenetic factor consistency for validate protocol for the evolution inference (based on logistic regression analysis).
Phylogenetic trees for each family will be extended to include strict consensus trees, and bootstrap analysis will be provided for Neighbor Joining and Maximum Parsimony trees.
Maximum Likelihood trees will be estimated using the PHYML software, also using evolutionary models selected. Maximum Parsimony trees will be estimated using the PAUP* software, by taking an extended majority rule consensus of the most parsimonious trees. All trees will be rooted using the midpoint method. Bayesian Inference trees will be estimated with MrBayes software.