Industrial-Strength String Manipulation

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Example: Bioinformatics

Here is the beginning of the string giving the genome of the SARS virus:

CTACCCAGGAAAAGCCAACCAACCTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTAGCTGTCGCTCG
GCTGCATGCCTAGTGCACCTACGCAGTATAAACAATAATAAATTTTACTGTCGTTGACAAGAAACGAGTAACTCGTCCCTCTT
CTGCAGACTGCTTACGGTTTCGTCCGTGTTGCAGTCGATCATCAGCATACCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAG
ATGGAGAGCCTTGTTCTTGGTGTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTCCTTCAGGTTAGAGACGTGCTAGT
GCGTGGCTTCGGGGACTCTGTGGAAGAGGCCCTATCGGAGGCACGTGAACACCTCAAAAATGGCACTTGTGGTCTAGTAGAGC
TGGAAAAAGGCGTACTGCCCCAGCTTGAACAGCCCTATGTGTTCATTAAACGTTCTGATGCCTTAAGCACCAATCACGGCCAC
AAGGT...

This finds short palindromes in the SARS genome:

In[1]:=

Out[1]:= {TCTTTCT, ACAAACA, CTCCCTC, TATTTAT, TCTTTCT, TCTTTCT, GTGGGTG, TCTTTCT, TCTTTCT, TGTTTGT, TATTTAT, ACAAACA, ACAAACA, TATTTAT, ACAAACA, ATAAATA, TCTTTCT, TGTTTGT, ACAAACA, TATTTAT, AAAAAAA, TTTTTTT, ATAAATA, ACAAACA, AGAAAGA, GAGGGAG, ACAAACA, AAAAAAA, AAAAAAA, AAAAAAA}

This finds long repeats:

In[2]:= StringCases[SARS, w : ((x_) ..) /; StringLength[w] > 5]

Out[2]:= {CCCCCC, GGGGGG, AAAAAAAA, TTTTTTT, TTTTTT, CCCCCC, AAAAAAAAAAAAAAAAAAAAAAAA}

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Example: Dictionary

Mathematica 5.1 comes with a 90,000-word English dictionary.

This finds all palindromic words in the dictionary.

In[3]:=

FindWords[x__ /; x == StringReverse[x]]

Out[3]:= {a, aha, aka, bib, bob, boob, bub, CFC, civic, dad, dd, deed, deified, did, dud, DVD, eke, ere, eve, ewe, eye, gag, gig, huh, I, kayak, kook, level, ma'am, madam, mam, MGM, minim, mom, mum, nan, non, noon, nun, oho, pap, peep, pep, pip, poop, pop, pup, radar, redder, refer, repaper, reviver, rotor, sagas, sees, seres, sexes, shahs, sis, solos, SOS, stats, stets, tat, tenet, tit, TNT, toot, tot, tut, wow, WWW}