Biology Reference
In-Depth Information
Table 3. List of Services at PathPort
Data:
Genome Search
Pathogen Background Information
Phylogenetic Tree construction
EBI (gene expression)
GEO (gene expresion)
Gene Prediction:
Genscan
Glimmer
GlimmerM
TigrScan
GrailEXP
GeneMark
Orpheus
Probe design:
PCR/Hybridization
YODA
DNA assembly, digestion:
Contigs from trace files
Restriction enzymes
tRNA
Transcription factors
Ribosomal RNA
Sequence Alignment and Search:
BLAST
FASTA
Smith-Waterman
CLUSTAL-W
Sean
Ssaha and SsahaSNP
MUMmer
InterProScan
Microarray analysis:
Agnes
Hclust
Kmean
Anova
Manova
Diana (Hierarchical clustering)
Multtest (f/t tests)
Rfda (Discriminant analysis)
Rknn (KNN classification)
Rlda (Supervised classification)
Rpca (PCA classification)
Rsom (Gene SOM)
Rsvm (SVM classification)
interactions gleaned from literature curation (Fig. 4). In order to pro-
mote interoperability, PathPort has developed the Molecular Interaction
Network Markup Language (MINetML), an XML-based data represen-
tation format along the lines of PIML. MINetML focuses on a high-
level description of the molecular and cellular interaction between
pathogen and host. It emphasizes curatorial accuracy and cross-refer-
encing to external databases and ontology systems.
Outreach Activities at PathPort
The PathPort project is committed to providing the scientific commu-
nity with integrated and easy access to the latest data and state-of-the-art
analysis tools. The project actively solicits feedback and suggestions
for improvement from PathPort users. Users may suggest features to
 
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