New Genomes in GenBank The following complete microbial genomes have been deposited recently in GenBank and can be viewed in Entrez Genome: Brucella melitensis: AE008917 and AE008918 Encephalitozoon cuniculi: AL391737 and AL590442-AL590451 Ralstonia solanacearum: AL646052 and AL646053 Agrobacterium tumefaciens C58: AE008687–AE008690 Base Quality in HTG Records The High-Throughput Genomic (HTG) division of GenBank contains unfinished sequence data submitted by large-scale sequencing centers. A typical HTG record might consist of first pass sequence data generated from a single cosmid, BAC, YAC, or P1 clone, and contain one or more gaps. HTG records contain a status indicator of Phase 0, Phase 1, or Phase 2. Phase 0 sequences are usually one-to-few pass reads of a single clone, so are usually not contigs. Phase 1 sequences are usually unordered, unoriented contigs, with gaps. Phase 2 sequences are usually ordered and oriented contigs, with or without gaps. In addition to the Phase information, submitters may include a Base Quality score, or PHRAP score, to indicate the quality of the sequence data. This base quality information can be viewed in Entrez. From the Display menu for HTG records, the “Base Quality” view option reports the PHRAP score for each base in a tabular format. The “Graphics” view presents a PHRAP trace for the sequence, with regions of lesser base quality showing up as depressions in the trace. |
New Sequin Release Enhances Sequence Updating and Feature Propogation Utilities Sequin version 3.70 for Macintosh, PC/MS Windows, and Unix Computers was made available from the NCBI FTP site recently. This version features new Update Sequence and Feature Propagation utilities. The revised Update Sequence utility is based on an alignment indexing function and offers new update possibilities. Users may now “patch” an internal fragment of the current sequence with a corrected sequence. It is also now possible to update with an ASN.1 file containing both sequence and features. This allows overlapping records to be merged. The revised Feature Propagation utility is found under the Edit menu of the Record Viewer. It was also rewritten with align-ment indexing. If you have selected a single feature in the record viewer, only that feature will be propagated. Otherwise, all features from the designated sequence are propagated to all other sequences. A new version of Sequin will be released shortly that features an updated alignment reader. The new reader uses intelligent parsing to read several text alignment formats, including Phylip, NEXUS, and FASTA+GAP, into ASN.1 Seq-aligns. The reader produces many different informative error messages, so that the user may identify and fix any subtle problems in the text alignment which prevent its successful conversion into a Seq-align. |
