Clustal W and Clustal X version 2.0

SUMMARY: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. AVAILABILITY: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/     

GenomeDiagram: a python package for the visualization of large-scale genomic data

SUMMARY: We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. AVAILABILITY: GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. SUPPLEMENTARY INFORMATION: A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.     

Sequence type analysis and recombinational tests (START).

The 32-bit Windows application START is implemented using Visual Basic and C(++) and performs analyses to aid in the investigation of bacterial population structure using multilocus sequence data. These analyses include data summary, lineage assignment, and tests for recombination and selection. AVAILABILITY: START is available at http://outbreak.ceid.ox.ac.uk/software.htm. CONTACT: keith.jolley@ceid.ox.ac.uk     

TetraploidMap for Windows: linkage map construction and QTL mapping in autotetraploid species

An earlier program, TetraploidMap, enabled linkage analysis to be performed for autotetraploid species, with a text-based input and output. The current program, TetraploidMap for Windows, is considerably enhanced, and now goes beyond linkage analysis to perform quantitative trait locus (QTL) interval mapping, with a range of models and thresholds assessed by permutation tests. A Windows-based interface facilitates data entry and exploration. TetraploidMap for Windows is freely available from the Web site of Bioinformatics and Statistics Scotland at http://www.bioss.ac.uk/ (user-friendly software).     

A database application for long‐term ecological field experiments

Problem: A series of long‐term field experiments is described, with particular reference to monitoring and quality control. This paper addresses problems in data‐management of particular importance for long‐term studies, including data manipulation, archiving, quality assessment, and flexible retrieval for analysis Method: The problems were addressed using a purpose‐built database system, using commercial software and running under Microsoft Windows. Conclusion: The database system brings many advantages compared to available software, including significantly improved quality checking and access. The query system allows for easy access to data sets thus improving the efficiency of analysis. Quality assessments of the initial dataset demonstrated that the database system can also provide general insight into types and magnitudes of error in data‐sets. Finally, the system can be generalised to include data from a number of different projects, thus simplifying data manipulation for meta‐analysis.     

SMART技术构建衣藻细胞的酵母双杂交文库

衣藻是用来研究植物光合作用和动物纤毛常用的模式生物.为了研究蛋白质之间的相互作用,利用SMART技术构建了衣藻的酵母双杂交文库.使用Trizol试剂提取鞭毛再生过程和光周期培养的细胞进入分裂前的衣藻细胞的总RNA,经过Oligotex纯化得到mRNA;应用SMART技术和LD-PCR合成双链cDNA,经过CHROMA SPIN TE-400柱子去除短片段的cDNA;cDNA和线性化载体pGADT7-Rec共转化酵母Y187构建酵母双杂交文库.库容达到3.0 × 106CFU,重组率为70％,插入片段平均长度为0.6 kb.以上结果说明该文库质量较好,能够通过筛选文库得到与目的蛋白互相作用的蛋白质,为寻找蛋白质的作用伴侣打下基础.     

Circles: automating the comparative analysis of RNA secondary structure

SUMMARY: Circles is a program for inferring RNA secondary structure using maximum weight matching. The program can read in an alignment in FASTA, ClustalW, or NEXUS format, compute a maximum weight matching, and export one or more secondary structures in various file formats. AVAILABILITY: The program is available at no cost from http://taxonomy.zoology.gla.ac.uk/rod/circles/ and requires Windows 95/98/NT. CONTACT: r.page@bio.gla.ac.uk     

CINEMA-MX: a modular multiple alignment editor

Analyzing and visualizing multiple sequence alignments is a common task in many areas of molecular biology and bioinformatics. Many tools exist for this purpose, but are not easily customizable for specific in-house uses. Here we report the development of an editor, CINEMA-MX, that addresses these issues. CINEMA-MX is highly modular and configurable, and we present examples to illustrate its extensibility. AVAILABILITY: The program and full source code, which are available from http://www.bioinf.man.ac.uk/dbbrowser/cinema-mx, are being released under a combination of the LGPL and GPL, for Unix or Windows platforms.     

Web watch

Teachers' websites

Webwise Spinneret Biology websitehttp://web.ukonline.co.uk/webwise/spinnere:

Lesson Planet www.lessonplanet.com

Gourmet Curriculum Press www.gourmetcurriculumpress.com

Learn.co.ukwww.learn.co.uk

Just for Teacherswww.justforteachers.co.uk     

DNAPlotter: circular and linear interactive genome visualization

Summary: DNAPlotter is an interactive Java application for generatingcircular and linear representations of genomes. Making use ofthe Artemis libraries to provide a user-friendly method of loadingin sequence files (EMBL, GenBank, GFF) as well as data fromrelational databases, it filters features of interest to displayon separate user-definable tracks. It can be used to producepublication quality images for papers or web pages. Availability: DNAPlotter is freely available (under a GPL licence)for download (for MacOSX, UNIX and Windows) at the WellcomeTrust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/circular/ Contact: artemis{at}sanger.ac.uk Associate Editor: John Quackenbush     

Protein analyst--a distributed object environment for protein sequence and structure analysis.

SUMMARY: Protein Analyst is a flexible tool for the analysis of protein sequences with emphasis on the integration of sequence and structural information. AVAILABILITY: The software will be available from the Oxford Molecular Biolib web site (http://www. oxmol.co.uk/biolib) and will be free to the academic research community.     

Comparative visualization of genetic and physical maps with Strudel

Data visualization can play a key role in comparative genomics, for example, underpinning the investigation of conserved synteny patterns. Strudel is a desktop application that allows users to easily compare both genetic and physical maps interactively and efficiently. It can handle large datasets from several genomes simultaneously, and allows all-by-all comparisons between these. Availability and implementation: Installers for Strudel are available for Windows, Linux, Solaris and Mac OS X at http://bioinf.scri.ac.uk/strudel/.     

SpecAlign--processing and alignment of mass spectra datasets

SUMMARY: Pre-processing of chromatographic profile or mass spectral data is an important aspect of many types of proteomics and biomarker discovery experiments. Here we present a graphical computational tool, SpecAlign, that enables simultaneous visualization and manipulation of multiple datasets. SpecAlign not only provides all common processing functions, but also uniquely implements an algorithm that enables the complete alignment of each mass spectrum within a loaded dataset. We demonstrate its utility by aligning two datasets each containing six spectra; one set was acquired prior to instrument calibration and the other following calibration. AVAILABILITY: The software is free of charge and available for download from http://ptcl.chem.ox.ac.uk/~jwong/specalign. Supports Windows operating systems including Windows 9X/NT/2000/XP.     

Flapjack--graphical genotype visualization

SUMMARY: New software tools for graphical genotyping are required that can routinely handle the large data volumes generated by the high-throughput single-nucleotide polymorphism (SNP) platforms, genotyping-by-sequencing and other comparable genotyping technologies. Flapjack has been developed to facilitate analysis of these data, providing real time rendering with rapid navigation and comparisons between lines, markers and chromosomes, with visualization, sorting and querying based on associated data, such as phenotypes, quantitative trait loci or other mappable features. AVAILABILITY: Flapjack is freely available for Microsoft Windows, Mac OS X, Linux and Solaris, and can be downloaded from http://bioinf.scri.ac.uk/flapjack .     

RALEE--RNA ALignment editor in Emacs

SUMMARY: Production of high quality multiple sequence alignments of structured RNAs relies on an iterative combination of manual editing and structure prediction. An essential feature of an RNA alignment editor is the facility to mark-up the alignment based on how it matches a given secondary structure prediction, but few available alignment editors offer such a feature. The RALEE (RNA ALignment Editor in Emacs) tool provides a simple environment for RNA multiple sequence alignment editing, including structure-specific colour schemes, utilizing helper applications for structure prediction and many more conventional editing functions. This is accomplished by extending the commonly used text editor, Emacs, which is available for Linux, most UNIX systems, Windows and Mac OS. AVAILABILITY: The ELISP source code for RALEE is freely available from http://www.sanger.ac.uk/Users/sgj/ralee/ along with documentation and examples. CONTACT: sgj@sanger.ac.uk     

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

The identification of proteins by mass spectrometry is a standard technique in the field of proteomics, relying on search engines to perform the identifications of the acquired spectra. Here, we present a user-friendly, lightweight and open-source graphical user interface called SearchGUI (http://searchgui.googlecode.com), for configuring and running the freely available OMSSA (open mass spectrometry search algorithm) and X!Tandem search engines simultaneously. Freely available under the permissible Apache2 license, SearchGUI is supported on Windows, Linux and OSX.     

Pedstrip: extracting a maximal subset of available,unrelated individuals from a pedigree

SUMMARY: Certain types of genetic analysis are simplified by assembling a collection of unrelated individuals, e.g. case-control experiments. If a family study is being performed then it will be necessary to extract subsets of unrelated, available individuals from pedigress. Our program provides an optimal method for performing this task. AVAILABILITY: The software is available, free of charge, on request from Oxagen Ltd. SUPPLEMENTARY INFORMATION: http://www.oxagen.co.uk     

Film News

Derek Baron, Trevor Bavage, Paul Butler, Andy Cooke, Zoe Crompton, Sam Ellis, Kevin Frobisher, Jean Martin, Mick Mulligan and Chris Ram; Andy Cooke and Jean Martin (Eds), 2002. Cambridge, UK: Cambridge University Press, pp. 558. £80. ISBN 0 521 75005 9.

Key Stage 3 Science Spectrum 7: Class Book Authors and publisher as above, 2002. £8.95. ISBN 0 521 75004 0. Reviewed by Leslie McRobert

Salters GCSE Science Volume 2: Student book Alexandra Clayton (Ed), 2002. Oxford, UK: Heinemann Educational Publishers, 211pp. £14.25 (10% educational discount on orders over £200, 12.5% 0ver £400). ISBN 0 435 629530. Reviewed by Pam Hillier

Modular Science for AQA: Year 11 Foundation and Higher Resource pack with CD-ROM Keith Hirst, Mike Hiscock, David Sang, Martin Stirrup, 2002. Oxford, UK: Heinemann Educational Publishers, 239pp. £109.99. ISBN 0 435 57199 0. Reviewed by Philip Loveday

Principles of Development (2nd Ed) Lewis Wolpert, Rosa Beddington, Thomas Jessell, Peter Lawrence, Elliot Meyerowitz, Jim Smith, 2002. Oxford, UK: Oxford University Press, 542pp. £75.00. ISBN 0-19-924939-3. Reviewed by Sofia Araujo

Enzyme Assays (2nd ed) R Eisenthal and M J Danson (eds), 2002. Oxford, UK: Oxford University Press, 282pp. £32.50. ISBN 0-19-963820-9. Reviewed by Roger Delpech

Gorilla Biology: A multidisciplinary perspective Andrea B Taylor and Michele L Goldsmith (eds), 2002. Cambridge, UK: Cambridge University Press, 528pp. £65.00. ISBN 0521792819. Reviewed by Pam Hillier

Gene therapy in the 21st Century — some perspectives 2001. Educational Broadcasting Services Trust, London. System requirements: PC: Windows 95/ 98/ NT; Internet Explorer V3, V4 or V 5.5. Minimum 166 MHz processor, 32 Mb RAM. Price: Two CD-ROMs; (UK Education) £25.00; (Non-UK Ed &; Europe) £55.00; (Outside EU) £75.00. Ordering: www.ebst.co.uk/pages/prod-edu.html#4, contact Jim@ebstrust.u-net.com. Reviewed by Gill Hickman

DNA and Proteins Oof Oud and Geoff Rickards, 2003. ETI Biodiversity Center, University of Amsterdam. ISBN 90-75000-62-6. System requirements: PC: Pentium running Windows 95, 98, ME, NT 3.5.1 or higher, 2000 or XP. 16 MB free application RAM. Display resolution: at least 800 x 600 pixels and 16 bit colour. Mac: PowerPC processor. Mac OS 7.6 or higher, or OS X (Classic). 16 MB free application RAM. Display resolution: at least 800 x 600 pixels and 16 bit colour. Price: £49.95 ex. VAT and P&;P for single user licence; £125 ex. VAT and P&;P for up to 5 users and £199 ex VAT and P&;P for up to 25 users at any one time. Note: IOB members can purchase the single user license for this resource at a cost of £44.95 ex VAT and P&;P. Ordering: Dr Bill Hominick, ETI Information Services Ltd., PO Box 3373, Wokingham, Berkshire, UK RG41 1XN; hominicks@ntlworld.com. Reviewed by Peter Anderson, John Cheverton, Peter Dreyer, Richard Greenway, Godfray Guilbert

Interactive Kidneys — The Biology Series; Keystage 4 2002. Birchfield Interactive, UK. System requirements: Microsoft Windows 95/ 98/ 2000/ ME/ XP or NT. 64 Megabytes RAM, 100 Megabytes of hard disk space. Note: for use on RM c-connect 3 networks users need read/write access to system and system32 folders. Price: £79.95 (includes site licence and five years of free upgrades). Ordering: www.birchfield.co.uk Reviewed by John Mynett

VirtualUnknown^TM Microbiology 2001. Intuitive Systems Inc., Texas, USA; Version 2.03BC, ISBN 0-8053-7598-8. System requirements: 180 MHz processor, 64 Mb RAM, Windows 95/98/NT/2000/ME, 800 × 600 pixels, CD-ROM Drive, printer. Ordering: Distributed through Benjamin Cummings and may be purchased with a textbook (Microbiology: An Introduction 8/E by Tortora, Funke &; Case) or as a standalone CD-ROM. Current prices are available at: www.aw.com/catalog. Reviewed by Richard Jenkins

Bodywise Original design by Simon and Adam Hosler; new material by Jen Phillips; updated design by Jen Phillips and Paul Hollin. 2001. Sherston Software Ltd, Malmesbury, UK. System requirements: PC:Windows 95 with Pentium P166 processor, 32MB RAM, a CD-ROM drive, 16-bit colour and soundcard. Mac: OS 7.6.1 or above, Power PC, 64MB available RAM, a CD-ROM drive, and 16-bit colour. Price: from £49.95 for a single user to £199.80 for unlimited users. Ordering: www.sherston.com Reviewed by Hilary MacQueen     

Inclusion counter: a public domain image analysis system for measurement of Chlamydiaceae growth in vitro

The traditional method of measuring chlamydial growth in vitro, counting Chlamydiaceae inclusions by eye, is time-consuming and error prone. This paper describes a novel automated image analysis system suitable for high-throughput screening of novel anti-Chlamydiaceae compounds. The software, Inclusion Counter v3.0, is freely available in the public domain (http://www.image-analysis.co.uk).     

The staden sequence analysis package

I describe the current version of the sequence analysis package developed at the MRC Laboratory of Molecular Biology, which has come to be known as the “Staden Package.” The package covers most of the standard sequence analysis tasks such as restriction site searching, translation, pattern searching, comparison, gene finding, and secondary structure prediction, and provides powerful tools for DNA sequence determination. Currently the programs are only available for computers running the UNIX operating system. Detailed information about the package is available from our WWW site: http://www.mrc-lmb.cam.ac.uk/pubseq/.