Workflows

mrFAST Indexing and Mapping (1)

• Download

This page contains a number of bioinformatics workflows based on the mrFAST sequence analysis package. This page describes Pipeline bioinformatics modules from the mrFAST suite.   mrFAST (micro-read Fast Alignment Search Tool) is mapper designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 6 bp. This manu...

Created: 2011-04-05 | Last updated: 2011-04-05

Credits: Pipeline

EMBOSS-Matcher Pipeline Workflow (1)

• Download

This page contains a number of bioinformatics workflows based on the advanced EMBOSS informatics package. This page describes as Pipeline modules several bioinformatics tools from the EMBOSS suite and demonstrates the construction of a couple of integrated pipeline workflows (end-to-end bioinformatics solutions via the LONI Pipeline). Matcher finds the best local alignments between two sequences. It can be used to compare two sequences looking for local sequence similarities using a ri...

Created: 2011-04-05 | Last updated: 2011-07-14

Credits: Pipeline

Bioinformatics BLAST processing Workflow (1)

• Download

This is a simple workflow demonstrating a sequence Basic Local Alignment Search Tool (BLAST). This workflow shows an example of a common bioinformatics pipeline workflow using tools from several different institutions. This workflow starts by formatting the NCIBI/NCBI Escherichia coli (E. coli) database, creating a database-index table, using a FASTA query instructions to create a filtering file, and finally running miBLAST, an efficient Basic Local Alignment Search Tool (BLAST) for batc...

Created: 2011-04-05 | Last updated: 2011-04-05

Credits: Pipeline

Parsed UniProt to PubMed (1)

• Download

Uses the parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve information from PubMed.

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Morgan Taschuk

Use UniProt to retrieve InterPro data (1)

• Download

Used parsed Uniprot results (see workflowUsed parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from InterPro.

Created: 2011-04-01

Credits: Morgan Taschuk

UniProt to Gene Ontology (1)

• Download

Used parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from Gene Ontology and outputs it in text format.

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Morgan Taschuk

Print Protein Information to HTML (1)

• Download

Takes in a lot of parameters in order to construct an HTML table to display the information.

Created: 2011-04-01

Credits: Morgan Taschuk

Odkrywanie reguł asocjacyjnych za pomocą... (1)

• Download

Proces pokazuje wykorzystanie algorytmu FP-Growth do odkrywania reguÅ‚ asocjacyjnych. Należy zwrócić uwagÄ™ na to, że implementacja algorytmu FP-Growth akceptuje jedynie atrybuty binominalne, zatem zachodzi konieczność zamiany wszystkich atrybutów numerycznych i nominalnych na binominalne.

Created: 2011-03-30 | Last updated: 2011-03-30

Vaccine Targets Workflow (3)

• Download

Comparison of the genome of Bacillus anthracis to closely related strains will allow the discovery of proteins which may be involved in pathogenicity. Based on the biochemical pathways where the protein interacts, vaccines can be designed for these unique proteins. By gaining insight into the biochemical pathways that the unique proteins are involved in, the proteins can also be assessed for potential quality as vaccines. The key components of the vaccine finding system are the following: T...

Created: 2011-03-30 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

Compile Protein FASTA from Target to Drug ... (1)

• Download

Uses a tab-delimited file with protein target and drug information (created in Ondex) to compile a protein FASTA file including each target.

Created: 2011-03-30 | Last updated: 2011-03-30

Credits: Morgan Taschuk Andrewsmeaton