Genomics and Bioinformatics: An Introduction to Programming Tools for Life Scientists
With the arrival of genomics and genome sequencing projects, biology has been transformed into an incredibly data-rich science. The vast amount of information generated has made computational analysis critical and has increased demand for skilled bioinformaticians. Designed for biologists without previous programming experience, this textbook provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout the book and are combined with practical bioinformatics examples, leading students through the process from biological problem to computational solution. All of the Perl scripts, sequence and database files used in the book are available for download at the accompanying website, allowing the reader to easily follow each example using their own computer. Programming examples are kept at an introductory level, avoiding complex mathematics that students often find daunting. The book demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems.
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Genes and genomes
Early days of restriction enzymes
functions and applications
Changes in EOXP2 specific to humans
Examination of the criminal case
details of family genetics l
Where are the crossingover sites?
brief Unix reference I
a selection of biological sequence analysis
a short Perl reference I
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amino acid analysis Appendix array bacterial base pairs bioinformatics biological BLAST search CAG repeats cancer cells characters chromosome ClustalW codon columns command line contains CpG islands disease DNA molecule DNA sequence domain encoding EOXP2 evolution example exons ferritin ﬁrst foreach format FOXP2 function GAATTC genetic code genetic information genome sequence hash human genome identify important individuals instance introns iron responsive element large number loop match matrix methods miRNA molecular mRNA mucin multiple alignment mutations NCBI nucleotide nucleotide sequence ofthe open(IN operator output Perl Perl code Perl program Perl script position previous chapter primers produce protein sequence PSSM query sequence referred region regular expression replaced restriction enzymes result RNAi sequence alignment sequence database shown siRNA SNPs species speciﬁc splice strand string structure substr swissprot symbol testseq thylacine transcription translation tree UniProt Unix variable viral