GLOSSARY .ace file – A computer file containing all of the sequence reads for a given project, often a fosmid or BAC clone. Aligned reads – Consed window that shows all of the reads in a particular region. This window shows low quality sequence in shades of gray, and high quality sequence in white. Assembly View – Consed window that shows the length and number of contigs based on the most recent Phred/Phrap compilation of sequence data. Forward/reverse pairs with reads in different contigs, and the amount of coverage are shown. Assembly – the ordered compilation of read data by Phred/Phrap that uses sequence matches, forward/reverse read pairs, etc. to determine read location and orientation in the contig. Autofinish – a computer program used to call reactions prior to a human finisher working on the sequence. It is fast, calls very efficient reactions, and tags editable regions for the human finisher to work on. BAC – Bacterial Artificial Chromosome. A large segment of DNA ranging in size from 100,000 to 200,000 bp in length that is propagated in bacteria. Chemistry – different mixtures of nucleotides used in sequencing reactions which yield better or worse results when dealing with problem regions. Commonly used chemistries include dGTP, Big Dye, and a 4:1 ratio of the two. Clone – E. coli or other host containing a single recombinant DNA molecule to be sequenced Complemented sequence match – A match reported in the Search for String window that finds the complementary sequence (sequence from the opposite strand) from that used to search in the consensus sequence of the assembly. Contrast with an Uncomplemented sequence match – A match reported in the Search for String window that finds the exact sequence used to search in the consensus sequence in the assembly. Consed – program used to view and edit the data assembled by Phred/Phrap.
GLOSSARY .ace file – A computer file containing all of the sequence reads for a given project, often a fosmid or BAC clone. Aligned reads – Consed window that shows all of the reads in a particular region. This window shows low quality sequence in shades of gray, and high quality sequence in white. Assembly View – Consed window that shows the length and number of contigs based on the most recent Phred/Phrap compilation of sequence data. Forward/reverse pairs with reads in different contigs, and the amount of coverage are shown. Assembly – the ordered compilation of read data by Phred/Phrap that uses sequence matches, forward/reverse read pairs, etc. to determine read location and orientation in the contig. Autofinish – a computer program used to call reactions prior to a human finisher working on the sequence. It is fast, calls very efficient reactions, and tags editable regions for the human finisher to work on. BAC – Bacterial Artificial Chromosome. A large segment of DNA ranging in size from 100,000 to 200,000 bp in length that is propagated in bacteria. Chemistry – different mixtures of nucleotides used in sequencing reactions which yield better or worse results when dealing with problem regions. Commonly used chemistries include dGTP, Big Dye, and a 4:1 ratio of the two. Clone – E. coli or other host containing a single recombinant DNA molecule to be sequenced Complemented sequence match – A match reported in the Search for String window that finds the complementary sequence (sequence from the opposite strand) from that used to search in the consensus sequence of the assembly. Contrast with an Uncomplemented sequence match – A match reported in the Search for String window that finds the exact sequence used to search in the consensus sequence in the assembly. Consed – program used to view and edit the data assembled by Phred/Phrap.
Guide_to_Consed.docx