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PECAAN Home

PECAAN Workflow Description

PECAAN Userguide and Examples

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PECAAN Acknowledgements

Contact Information

PECAAN Overview

The Science Education Alliance PHAGES program has adopted a standard workflow for the identification of gene locations within newly sequenced phage genomes. This workflow uses several programs to locate and archive the gene locations including DNA Master [1], Glimmer [2], GeneMark [3], and Aragorn [4]. Functional annotations are added to genes by identifying significant matches to other proteins with known functions through queries to databases at Phagesdb.org [5], NCBI [6], CDD [7] and HHPred [8]. Annotation evidence is typically recorded in student notebooks and/or electronic files that allow others to check the annotations before publication of the annotated phage genome in GenBank. The quality control review of each annotated genome can be arduous, depending on the quality, completeness and consistency of the annotation evidence recorded by the students. PECAAN was developed to facilitate the collection of gene evidence and to implement a consistent presentation during the annotation and the quality control review of the annotation. This database driven web application runs on many web-enabled devices including laptops, tablets and phones that use an html5 compliant browser. PECAAN has been implemented in the Bioinformatic 312 laboratory at Western Kentucky University and has greatly facilitated the speed and accuracy of both the annotation process and review of our newly sequenced mycobacteriophage genomes.

To gain access to the PECAAN network, click on the "Join the Nuts" like at the left.

PECAAN and DNA Master Workflows

PECAAN Workflow Comparison to DNA Master

References

1. DNA Master, http://cobamide2.bio.pitt.edu/
2. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL: Improved microbial gene identification with GLIMMER. Nucl. Acids Res. 1999, 27:4636-4641. https://ccb.jhu.edu/software/glimmer/
3. Lukashin A, Borodovsky M: Genemark.hmm: new solutions for gene finding. Nucl. Acids Res. 1998, 26:1107-1115. http://exon.gatech.edu/GeneMark/heuristic_gmhmmp.cgi
4. Laslett D, Cangack B: ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucl. Acids Res. 2004, 32:11-16. http://mbio-serv2.mbioekol.lu.se/ARAGORN/
5. http://phagesdb.org/blastp/
6. http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
7. http://www.ncbi.nlm.nih.gov/cdd/
8. http://toolkit.tuebingen.mpg.de/hhpred