dorsal/arxiv
View SchemaClone-array pooled shotgun mapping and sequencing: design and analysis of experiments
| Authors | Miklós Csürös, Bingshan Li, Aleksandar Milosavljevic |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0312017 |
| URL | https://arxiv.org/abs/q-bio/0312017 |
Abstract
This paper studies sequencing and mapping methods that rely solely on pooling and shotgun sequencing of clones. First, we scrutinize and improve the recently proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a BAC-linked assembly of a whole genome sequence. Secondly, we introduce a novel physical mapping method, called Clone-Array Pooled Shotgun Mapping (CAPS-MAP), which computes the physical ordering of BACs in a random library. Both CAPSS and CAPS-MAP construct subclone libraries from pooled genomic BAC clones. We propose algorithmic and experimental improvements that make CAPSS a viable option for sequencing a set of BACs. We provide the first probabilistic model of CAPSS sequencing progress. The model leads to theoretical results supporting previous, less formal arguments on the practicality of CAPSS. We demonstrate the usefulness of CAPS-MAP for clone overlap detection with a probabilistic analysis, and a simulated assembly of the Drosophila melanogaster genome. Our analysis indicates that CAPS-MAP is well-suited for detecting BAC overlaps in a highly redundant library, relying on a low amount of shotgun sequence information. Consequently, it is a practical method for computing the physical ordering of clones in a random library, without requiring additional clone fingerprinting. Since CAPS-MAP requires only shotgun sequence reads, it can be seamlessly incorporated into a sequencing project with almost no experimental overhead.
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"date_created": "2026-03-02T18:01:31.612000Z",
"date_modified": "2026-03-02T18:01:31.612000Z",
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"abstract": "This paper studies sequencing and mapping methods that rely solely on pooling\nand shotgun sequencing of clones. First, we scrutinize and improve the recently\nproposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a\nBAC-linked assembly of a whole genome sequence. Secondly, we introduce a novel\nphysical mapping method, called Clone-Array Pooled Shotgun Mapping (CAPS-MAP),\nwhich computes the physical ordering of BACs in a random library. Both CAPSS\nand CAPS-MAP construct subclone libraries from pooled genomic BAC clones.\n We propose algorithmic and experimental improvements that make CAPSS a viable\noption for sequencing a set of BACs. We provide the first probabilistic model\nof CAPSS sequencing progress. The model leads to theoretical results supporting\nprevious, less formal arguments on the practicality of CAPSS. We demonstrate\nthe usefulness of CAPS-MAP for clone overlap detection with a probabilistic\nanalysis, and a simulated assembly of the Drosophila melanogaster genome. Our\nanalysis indicates that CAPS-MAP is well-suited for detecting BAC overlaps in a\nhighly redundant library, relying on a low amount of shotgun sequence\ninformation. Consequently, it is a practical method for computing the physical\nordering of clones in a random library, without requiring additional clone\nfingerprinting. Since CAPS-MAP requires only shotgun sequence reads, it can be\nseamlessly incorporated into a sequencing project with almost no experimental\noverhead.",
"arxiv_id": "q-bio/0312017",
"authors": [
"Mikl\u00f3s Cs\u00fcr\u00f6s",
"Bingshan Li",
"Aleksandar Milosavljevic"
],
"categories": [
"q-bio.GN"
],
"title": "Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments",
"url": "https://arxiv.org/abs/q-bio/0312017"
},
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