Contigs built with fingerprints, markers, and FPC V4.7.

By Carol Soderlund, S. Humphray, A. Dunham, L. French. Genome Research, 2000

350 citations recorded by the source corpus.

Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/227b75c9af6a53e103dbaab69ee1de808a5796dd

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In Molecular Biology

Citations in the corpus

Development of Genetic and Genomic Research Resources for Brachypodium distachyon, a New Model System for Grass Crop Research (2008, neutral): “Based on shared fi ngerprint patterns, clones derived from the same regions of a genome can be assembled into contigs (Soderlund et al., 2000).”
A Snapshot of the Emerging Tomato Genome Sequence (2009, methodology): “All BACs from the HindIII library and from the MboI library were fi ngerprinted and contigs of overlapping BACs were generated using the fi ngerprinted contigs (FPC) tool (Soderlund et al., 2000).”
SyMAP v3.4: a turnkey synteny system with application to plant genomes (2011, methodology): “SyMAP (1) is a distributable software package that was originally developed to compute synteny blocks between a sequenced genome and a Fingerprint Contigs (FPC) map (2,3), and has been extended to support pairs of large sequenced genomes, with special attention to plant genomes.”
Genome sequence of the palaeopolyploid soybean (2010, background): “BMC Genomics (submitted) Hyten DL, Choi I-Y, Song Q, Specht JE, Carter TE, Shoemaker RC, Hwang E-Y, Matukumalli LK, Cregan PB (2009) A high density integrated genetic linkage map of soybean and the development of a 1,536 Universal Soy Linkage Panel for QTL mapping. Genetics (submitted) Jaffe DB, But”