Consed
Encyclopedia
Consed is a program for viewing, editing, and finishing DNA sequence assemblies
. Originally developed for sequence assemblies created with phrap
, recent versions also support other sequence assembly programs like Newbler.
. At genome sequencing centers, Consed was used to check assemblies generated by phrap
, solve assembly problems like those caused by highly identical repeats, and finishing tasks like primer picking and gap closure.
Development of Consed has continued after the completion of the Human Genome Project
. Current Consed versions support very large projects with millions of reads, enabling the use with newer sequencing methods like 454 sequencing
and Solexa sequencing. Consed also has advanced tools for finishing tasks like automated primer picking
Sequence assembly
In bioinformatics, sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 1000 bases,...
. Originally developed for sequence assemblies created with phrap
Phrap
Phrap is a widely used program for DNA sequence assembly. It is part of the Phred-Phrap-Consed package.- History :Phrap was originally developed by Prof. Phil Green for the assembly of cosmids in large-scale cosmid shotgun sequencing within the Human Genome Project...
, recent versions also support other sequence assembly programs like Newbler.
History
Consed was originally developed as a contig editing and finishing tool for large-scale cosmid shotgun sequencing in the Human Genome ProjectHuman Genome Project
The Human Genome Project is an international scientific research project with a primary goal of determining the sequence of chemical base pairs which make up DNA, and of identifying and mapping the approximately 20,000–25,000 genes of the human genome from both a physical and functional...
. At genome sequencing centers, Consed was used to check assemblies generated by phrap
Phrap
Phrap is a widely used program for DNA sequence assembly. It is part of the Phred-Phrap-Consed package.- History :Phrap was originally developed by Prof. Phil Green for the assembly of cosmids in large-scale cosmid shotgun sequencing within the Human Genome Project...
, solve assembly problems like those caused by highly identical repeats, and finishing tasks like primer picking and gap closure.
Development of Consed has continued after the completion of the Human Genome Project
Human Genome Project
The Human Genome Project is an international scientific research project with a primary goal of determining the sequence of chemical base pairs which make up DNA, and of identifying and mapping the approximately 20,000–25,000 genes of the human genome from both a physical and functional...
. Current Consed versions support very large projects with millions of reads, enabling the use with newer sequencing methods like 454 sequencing
454 Life Sciences
454 Life Sciences, is a biotechnology company based in Branford, Connecticut. It is a subsidiary of Roche, and specializes in high-throughput DNA sequencing.-History and Major Achievements:...
and Solexa sequencing. Consed also has advanced tools for finishing tasks like automated primer picking