sim4
tool for aligning cDNA and genomic DNA
Install
- All systems
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curl cmd.cat/sim4.sh
- Debian
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apt-get install sim4 - Ubuntu
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apt-get install sim4 - Kali Linux
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apt-get install sim4 - Windows (WSL2)
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sudo apt-get updatesudo apt-get install sim4 - Raspbian
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apt-get install sim4 - Dockerfile
- dockerfile.run/sim4
sim4
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.