Imuroi lähdekoodipaketti sim4:
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.
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| Arkkitehtuuri | Paketin koko | Koko asennettuna | Tiedostot |
|---|---|---|---|
| alpha | 59.0 kt | 164 kt | [tiedostoluettelo] |
| amd64 | 53.4 kt | 144 kt | [tiedostoluettelo] |
| armel | 52.8 kt | 140 kt | [tiedostoluettelo] |
| avr32 (epävirallinen siirros) | 56.0 kt | 124 kt | [tiedostoluettelo] |
| hppa | 53.9 kt | 140 kt | [tiedostoluettelo] |
| hurd-i386 | 47.8 kt | 132 kt | [tiedostoluettelo] |
| i386 | 48.8 kt | 132 kt | [tiedostoluettelo] |
| ia64 | 75.8 kt | 220 kt | [tiedostoluettelo] |
| kfreebsd-amd64 | 54.1 kt | 122 kt | [tiedostoluettelo] |
| kfreebsd-i386 | 49.1 kt | 110 kt | [tiedostoluettelo] |
| m68k (epävirallinen siirros) | 42.4 kt | 124 kt | [tiedostoluettelo] |
| mips | 55.2 kt | 160 kt | [tiedostoluettelo] |
| mipsel | 55.9 kt | 164 kt | [tiedostoluettelo] |
| powerpc | 53.5 kt | 144 kt | [tiedostoluettelo] |
| s390 | 51.4 kt | 140 kt | [tiedostoluettelo] |
| sparc | 49.2 kt | 136 kt | [tiedostoluettelo] |