Academic Journal
PGAAS: a prokaryotic genome assembly assistant system
| العنوان: | PGAAS: a prokaryotic genome assembly assistant system |
|---|---|
| المؤلفون: | Yu, Z, Li, T, Zhao, JD, Luo, JC |
| المساهمون: | Luo, JC (reprint author), Peking Univ, Coll Life Sci, Beijing 100871, Peoples R China., Peking Univ, Coll Life Sci, Beijing 100871, Peoples R China., Peking Univ, Natl Key Lab Prot Engn & Plant Genet Engn, Beijing 100871, Peoples R China. |
| المصدر: | SCI |
| بيانات النشر: | bioinformatics |
| سنة النشر: | 2002 |
| المجموعة: | Peking University Institutional Repository (PKU IR) / 北京大学机构知识库 |
| مصطلحات موضوعية: | TOOL |
| الوصف: | Motivation: In order to accelerate the finishing phase of genome assembly, especially for the whole genome shotgun approach of prokaryotic species, we have developed a software package designated prokaryotic genome assembly assistant system (PGAAS). The approach upon which PGAAS is based is to confirm the order of contigs and fill gaps between contigs through peptide links obtained by searching each contig end with BLASTX against protein databases. Results: We used the contig dataset of the cyanobacterium Synechococcus sp. strain PCC7002 (PCC7002), which was sequenced with six-fold coverage and assembled using the Phrap package. The subject database is the protein database of the cyanobacterium, Synechocystis sp. strain PCC6803 (PCC6803). We found more than 100 non-redundant peptide segments which can link at least 2 contigs. We tested one pair of linked contigs by sequencing and obtained satisfactory result. PGAAS provides a graphic user interface to show the bridge peptides and pier contigs. We integrated Primer3 into our package to design PCR primers at the adjacent ends of the pier contigs. ; Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability ; SCI(E) ; 6 ; 5 ; 661-665 ; 18 |
| نوع الوثيقة: | journal/newspaper |
| اللغة: | English |
| تدمد: | 1367-4803 |
| Relation: | BIOINFORMATICS.2002,18,(5),661-665.; 763325; http://hdl.handle.net/20.500.11897/388284; WOS:000176226800003 |
| DOI: | 10.1093/bioinformatics/18.5.661 |
| الاتاحة: | https://hdl.handle.net/20.500.11897/388284 https://doi.org/10.1093/bioinformatics/18.5.661 |
| رقم الانضمام: | edsbas.C8808902 |
| قاعدة البيانات: | BASE |
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