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xContents16. Analysis of Transposable Element Sequences Using CENSORand RepeatMasker. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323Ahsan Huda and I. King Jordan17. DNA Sequence Polymorphism Analysis Using DnaSP . . . . . . . . . . . . . . . . . . . . . . 337Julio RozasIndex ............................................................. 351
Page 4: M ETHODS IN M OLECULAR B IOLOGY TMB
Page 10: PrefaceThe recent accumulation of i
Page 18: ContributorsFEDERICO ABASCAL • De
Page 22: ContributorsxiiiJESSE ZANEVELD •
Page 26: 2 Menlove, Clement, and CrandallBy
Page 30: 4 Menlove, Clement, and CrandallTab
Page 34: 6 Menlove, Clement, and CrandallFig
Page 38: 8 Menlove, Clement, and CrandallTab
Page 42: 10 Menlove, Clement, and CrandallFi
Page 46: 12 Menlove, Clement, and CrandalllH
Page 52: Similarity Searching Using BLAST 15
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24 Egan et al.challenges faced by t
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26 Egan et al.trees (termed guide t
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Gene Orthology Assessment with Orth
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Chapter 3Multiple Alignment of DNA
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Multiple Alignment of DNA Sequences
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Chapter 4SeqVis: A Tool for Detecti
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SeqVis: Tool for Detecting Composit
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82 Jermiin et al.points, and (ii) t
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84 Jermiin et al.ATBTGGCACACTDTGGCA
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86 Jermiin et al.3. Because the Cap
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88 Jermiin et al.construction. Syst
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90 Jermiin et al.69. Preparata, G.,
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Chapter 5Selection of Models of DNA
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Selection of Models of DNA Evolutio
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Chapter 6Estimating Maximum Likelih
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Estimating Maximum Likelihood Phylo
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140 Creevey and McInerneyFig. 7.1.
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142 Creevey and McInerneyapproach i
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144 Creevey and McInerneygenomes se
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146 Creevey and McInerneymore detai
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148 Creevey and McInerney2. Program
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158 Creevey and McInerneyThe second
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160 Creevey and McInerneygenomes: t
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Chapter 8Detecting Signatures of Se
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Detecting Signatures of Selection f
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186 MartinAt its very core the dete
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188 MartinFig. 9.2. The General set
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190 MartinBOOTSCAN windows should b
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192 Martinreason is that RDP3 ident
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194 Martinthe other indicating a cl
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196 Martinunique recombination even
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198 Martin3. Examples3.1. Producing
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200 Martinpointer over the left mos
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202 MartinFig. 9.5. Comparing recom
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204 Martinphylogenetic trees that t
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Chapter 10CodonExplorer: An Interac
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CodonExplorer 209selection and muta
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CodonExplorer 211Example: Searching
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CodonExplorer 2132.2. Output Option
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CodonExplorer 215Fig. 10.7. Selecti
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CodonExplorer 217in each gene into
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CodonExplorer 219Fig. 10.8. The cod
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CodonExplorer 221between a subset o
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CodonExplorer 223pull-down menu. Se
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CodonExplorer 225Fig. 10.13. Finger
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CodonExplorer 227checkbox, the desi
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CodonExplorer 2294. For details on
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CodonExplorer 2314. Efstratiadis, A
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Chapter 11Genetic Code Prediction f
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Genetic Code Prediction for Metazoa
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Chapter 12Computational Gene Annota
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Computational Gene Annotation 245De
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Computational Gene Annotation 2473.
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Computational Gene Annotation 249in
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Computational Gene Annotation 2513.
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Computational Gene Annotation 253Fi
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Computational Gene Annotation 25910
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Computational Gene Annotation 26129
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264 Mariño-Ramírez et al.lower eu
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266 Mariño-Ramírez et al.The anne
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268 Mariño-Ramírez et al.Fig. 13.
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270 Mariño-Ramírez et al.$aglam
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272 Mariño-Ramírez et al.individu
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274 Mariño-Ramírez et al.Fig. 13.
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276 Mariño-Ramírez et al.Yamamoto
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278 PevsnerThere are currently thre
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280 PevsnerFig. 14.1. A portion of
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282 Pevsnerand sequencing tracks (a
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284 Pevsnerqueries). For DNA querie
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286 PevsnerFor the top entry having
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288 PevsnerFig. 14.6. The Table Bro
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290 PevsnerComparative Genomics; tr
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292 Pevsner5 0 -TCCTTGCCACGGGCCACCA
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294 Pevsnercan differ dramatically
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296 Pevsner(a)(b)(c)Fig. 14.10. Cre
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298 PevsnerView the custom tracks.
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300 PevsnerTrevanion, S., Ureta-Vid
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Chapter 15Mining for SNPs and SSRs
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Mining for SNPs and SSRs 305routine
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Mining for SNPs and SSRs 307remains
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Mining for SNPs and SSRs 3092.1. SN
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Mining for SNPs and SSRs 311GC cont
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Mining for SNPs and SSRs 313Fig. 15
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Mining for SNPs and SSRs 315Table 1
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Mining for SNPs and SSRs 317Fig. 15
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Mining for SNPs and SSRs 319all pol
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Mining for SNPs and SSRs 32127. Kat
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324 Huda and JordanTE-related seque
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326 Huda and Jordansequences (i.e.,
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328 Huda and Jordan2.1.5. Method CE
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330 Huda and JordanFig. 16.1. CENSO
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332 Huda and JordanFig. 16.4. CENSO
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334 Huda and JordanFig. 16.7. Repea
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336 Huda and JordanReferences1. Lan
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338 RozasDNA polymorphism informati
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340 Rozasplotted. In this section,
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342 RozasThe raggedness r statistic
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344 Rozasdistribution of D. This di
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346 Rozasempirical distribution of
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348 Rozas3. Nucleotide diversity ca
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350 Rozas12. Swofford, D. L. (1998)
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352BIOINFORMATICS FOR DNA SEQUENCE
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354BIOINFORMATICS FOR DNA SEQUENCE
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