Direct GO count graphs were created to categorize the sequences to several groups based on their biological processes, molecular functions and cellular component ontologies.
Direct GO count graphs were created to categorize the sequences based on their biological processes and molecular functions as well as their cellular component.
To categorize the sequences into subfamilies, the classification criteria were that they must have at least four of the five best hits from the same subfamily in the BLASTP search.
We identified repeat elements from rhesus macaque bacterial artificial chromosome (BAC) sequence data initially using Repeatmasker Web Server, categorizing the sequence as human.
REPuter [36] was used to categorize the DNA sequence repeats within the genomes of the nine genomes of H. pylori.
To categorize the biological functions inferred from sequence similarity, Gene Ontology (GO) terms were assigned to transcripts matching GO-annotated records in the UniProt database.
To categorize the ABC transporters, amino acid sequences of known fungal ABC transporters from F. graminearum, A. nidulans and Neurospora crassa[ 25] were used as references to generate a phylogenetic tree.
The genomes of influenza A and B are composed of eight segments, and we first selected ca. 25,000 strains with a full set of eight sequences, categorized the full genome sequences according to host and serological type, and grouped them in each year.
For each unigene hit by EMS, the longest stretch of open reading frame was extracted using a custom perl script to categorize these sequence changes as synonymous or non-synonymous.
Nonetheless, using RaXML [ 27], we categorized the newly identified sequences into four clades and using ProtTest [ 44] we identified "PROTGAMMAWAGF" as the best-fit model.
The low level of erroneous or chimeric categorization shows that PolyCat successfully categorized the vast majority of sequence reads.
