First Printing: May/June 2004.
- Page 2: caption to Figure 1.1 should read: "two hydrogen bonds", not "three". Note: this is the "critical error" referred to in the BioMedical Engineering Online review.
- Page 47: exercise 3 incorrectly directs the reader to Appendix A. The list of Perl Operators can be found in Appendix B on page 457.
- Page 167: the location for the PDB files is incorrect. For example: ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb1m7t.ent.Z should be ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb/pdb1m7t.ent.Z. (Thanks for Dennis German for finding this one).
- Page 190: the table at the bottom of the page, columns 1-6 should read ATOM, not "ATOM(s).
- Page 257: the get_dna_crossrefs program fails to work when there's no "DR" lines in the EMBL data-file (note: the use of "DR" lines in EMBL data-files is going out-of-fashion; "\db_xref" lines are used instead). An updated version of this program (called get_dna_crossrefs2) fixes this problem, but can produce duplicate cross-references in its results (when the EMBL data-file contains both "DR" and "\db_xref" entries). To fix the duplicate problem, run the results of the updated program through the Linux sort command, thus: perl get_dna_crossrefs2 *EMBL* | sort -u which removes any duplicates found. (Thanks to Susan Tzotzos for bringing this to our attention).
- Page 297: bottom of page, start of chapter. The Internet address should read: http://srs.ebi.ac.uk.
- Page 383: bottom of page, underneath the (bits) column, 182 should be aligned underneath 183.
- Page 435: start of first paragraph should read: "Selecting: File Setup displays the Grace: Device setup dialog, ... ". The emphasis (bold/italic) in the text is all wrong.
- Page 451: near bottom of page, should read: "perldoc Bio::SearchIO". (Thanks to Heikki Lehväslaiho for pointing this out).
- Back cover: under Working with Applications, should read "An introduction to the important Bioperl Project concludes this part and rounds off the book." as opposed to " ... concludes this chapter ... ".
- Back cover: bottom left, Cover design by Dan Jubb should read Cover design by Dan Jubb, based on an original concept by Michael Moorhouse. Here is a graphic showing Michael's original concept and what it turned into.
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