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[ 原始碼: sim4  ]

套件: sim4 (0.0.20030921-3)

sim4 的相關超連結

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tool for aligning cDNA and genomic DNA

sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e., the start of one sequence overlaps the end of the other).

sim4 employs a blast-based technique to first determine the basic matching blocks representing the "exon cores". In this first stage, it detects all possible exact matches of W-mers (i.e., DNA words of size W) between the two sequences and extends them to maximal scoring gap-free segments. In the second stage, the exon cores are extended into the adjacent as-yet-unmatched fragments using greedy alignment algorithms, and heuristics are used to favor configurations that conform to the splice-site recognition signals (GT-AG, CT-AC). If necessary, the process is repeated with less stringent parameters on the unmatched fragments.

標籤: 領域: 生物學, 生物資訊學, 實做語言: C, 使用者介面: 命令行, 角色: 程式, 範圍: 實用程式, Purpose: Comparing, 搜尋, 支援的格式: 純文字

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硬體架構 套件大小 安裝後大小 檔案
kfreebsd-i386 49.1 kB110.0 kB [文件列表]