An unreal world awaits your Sim, and when you stumble upon the secret portal, there are mystical discoveries at every turn. Interact with familiars, cast spells on Sims around you, and concoct potions for friends and enemies. Study up on classic teachings, get sorcerous experts to train your Sim, and become a Spellcaster by completing a quest. Collect and cast spells to make Sims fight, conjure food, or even turn others into objects. Create drinkable potions to make Sims fall in love, remove unwanted curses, or live forever! Get in the spirit of sorcery with outfits that suit your Sim. Over-the-top attire is cauldron-ready, while a subdued ensemble is perfect for casting new spells. Collect wands and brooms to finish the look, then decorate rooms with enchanting objects.
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). If seqfile2 is a database of sequences, the sequence in seqfile1 will be aligned with each of the sequences in seqfile2.
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.
By default, sim4 searches both strands and reports the best match, measured by the number of matching nucleotides found in the alignment. The R command line option can be used to restrict the search to one orientation (strand) only.
Currently, five major alignment display options are supported, controlled by the A option. By default (A=0), only the endpoints, overall similarity, and orientation of the introns are reported. An arrow sign (->' or<-‘) indicates the orientation of the intron (+' or-‘ strand), when the signals flanking the intron have three or more position matches with either the GT-AG or the CT-AC splice recognition signals. When the same number of matches is found for both orientations, the intron is reported as ambiguous, and represented by --'. The sign==’ marks the absence from the alignment of a cDNA fragment starting at that position. Alternative formats (lav-block format, text, PipMaker-type `exons file’, or certain combinations of these options) can be requested by specifying a different value for A.
If the P option is specified with a non-zero value, sim4 will remove any 3′-end poly-A tails that it detects in the alignment.
Occasionally, sim4 may miss an internal exon when surrounded by very large introns, typically longer than 100 Kb. When this is suspected, the H option can be used to reset the exons’ weight to compensate for the intron gap penalty.
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