From Heather.Vincent from manchester.ac.uk Tue Jan 4 03:44:15 2011 From: Heather.Vincent from manchester.ac.uk (Heather Vincent) Date: Thu Jan 6 06:57:27 2011 Subject: [Arthropod] Introduction to microarray data analysis, and other distance learning courses Message-ID: <4D22DDDF.9030503@manchester.ac.uk> Members of this group might be interested in one or more of the online courses offered by the University of Manchester, UK. The courses beginning in March 2011 include 'Introduction to microarray data analysis' (http://octette.cs.man.ac.uk/bioinformatics/modules/BIOL61010.html) and 'Mathematics for metabolic modelling'. The maths course will prepare people for 'Computational Systems Biology', which will be running again in October. There are links to all of our distance courses here : http://octette.cs.man.ac.uk/bioinformatics/modules/index.html If you have any questions, or would like advice on the options, please contact the office for Advanced Professional Education (ape@cs.man.ac.uk). From bryony from seasurvey.co.uk Thu Jan 6 04:47:22 2011 From: bryony from seasurvey.co.uk (Bryony Pearce) Date: Thu Jan 6 06:57:40 2011 Subject: [Arthropod] Discovering Amphipod Families Message-ID: <4D258FAA.1010008@seasurvey.co.uk> Dear All, Thank you for supporting the development of the MESL School of Marine Taxonomy. Thingsare really starting to take off now and I am pleased to announce that we are now taking bookings for our "Discovering Amphipod Families " course which will be held over the first weekend in February. Details will go up on our website next week but if you know you would like a place on this course please do feel free to e.mail me directly for a booking form. *Discovering Amphipod Families*****Booking Now******* *4th -6th February** Marine Ecological Surveys Ltd, 3 Palace Yard Mews, Bath, BA1 2NH* This course will enable participants to gain experience and confidence in the identification, to the family level, of British marine Gammarid amphipods. The Gammarid amphipods are a large and diverse group of crustaceans, the identification of which which can be daunting for beginners to macrofaunal taxonomy. There are dozens of amphipod families, and hundreds of amphipod species found in UK waters and their identification requires microscopic examination of very small body parts. This course will guide students through the morphology of amphipods focusing on features used in identification at the family level. The course will use the key text for this field, the 1977 book of British Marine Amphipoda: Gammaridea by Roger J. Lincoln. Many taxonomic papers have been written since clarifying or changing details but this text remains the most comprehensive and accessible key for this group. The workshop will be predominantly lab based with microscope sessions guided by experienced senior taxonomists from the MESL laboratory team and utilising specimens from our in-house reference collection. Becoming familiar with the general morphology of amphipods, and identification to the family level, is a crucial step towards in the development of the skills required to accurately identify these animals to species. Please log on to our website for more detailed information and booking details www.seasurvey.co.uk. Wishing you all a very merry Christmas and a prosperous New Year Best Regards Bryony -- Bryony Pearce BSc (Hons) Research Director Marine Ecological Surveys Ltd 3 Palace Yard Mews Bath BA1 2NH Tel: 01225 442211 E.Mail: bryony@seasurvey.co.uk www.seasurvey.co.uk From gilbertd from net.bio.net Fri Jan 14 15:21:49 2011 From: gilbertd from net.bio.net (Don Gilbert) Date: Fri Jan 14 15:23:13 2011 Subject: [Arthropod] EvidentialGene : Evidence Directed Gene predictions for Arthropods Message-ID: <201101142021.p0EKLnv14240@net.bio.net> Dear genomicists and genome informaticians, I've been working on practical use of gene prediction/annotation methods for arthropods for over 6 years now, and gotten to the point where this recipe works well, and can be generally useful for eukaryote genome annotations: EvidentialGene : Evidence Directed Gene predictions for Eukaryotes See http://arthropods.eugenes.org/genes2/ This is similar to others' genome annotation protocols, but differs in some of the gory details. In particular, it is designed for parallel genome analyses on computer grids and clusters, it handles the large volumes of RNA-seq data now being churned out (sort of, still working to improve aspects), and it has a specially designed "Best Evidential Gene" picking algorithm included as a last step in combining/filtering gene prediction sets. This is not yet a pipeline package, not something that others can run as a black box, where you feed in data and it spits out shiny new annotated gene sets. But it is a recipe with detailed steps that work for the eukaryotes I've tested it on. A few colleagues have given this recipe a beginning try; with some effort it appears that others can use this. So far we have applied it to Daphnia pulex and Daphnia magna, Pea aphid, Nasonia jewel wasp, and Theobroma cacao (the chocolate tree, where this worked well). Just now there is one fully worked public example at above URL, for Pea aphid. Final gene models for aphid are still in progress, from lots of new rna-seq evidence. The documentation is in a rough state. This document has gory details for pea_aphid annotations, http://arthropods.eugenes.org/genes2/pea_aphid2/docs/ aphid-genes-details.txt This will perhaps be of most use now to those of you who already are doing informatics of genome annotations, and know some of these methods. There may be parts of this you can incorporate or learn from. If you have interests in this, feel free to contact me. Don Gilbert, gilbertd at indiana edu -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@indiana.edu--http://marmot.bio.indiana.edu/ From bryony from seasurvey.co.uk Mon Jan 17 07:15:39 2011 From: bryony from seasurvey.co.uk (Bryony Pearce) Date: Mon Jan 17 12:01:05 2011 Subject: [Arthropod] MESL School of Taxonomy - New Courses Announced Message-ID: <4D3432EB.5090305@seasurvey.co.uk> Dear All, Happy New Year! I hope that the Christmas period treated you well! I just wanted to let you know that we still have a limited number of places available on our "Discovering Amphipod Families " course and I also have the great pleasure of announcing two more taxonomy courses for which we are now taking bookings. The first is a Terebellomoprha and Nephtyidae identification course which will be lead by Dr.Sc. Igor Jirkov, an international authority on these groups from Moscow State Lomonosov University. The second is our two-week benthic taxonomy school which will be held at the Marine Biological Association of the Uk in June. Full details will be on our website shortly but if you know you would like a place on either of these courses please do feel free to e.mail me directly for a booking form. *Discovering Amphipod Families*****Booking Now******* *4th -6th February** Marine Ecological Surveys Ltd, 3 Palace Yard Mews, Bath, BA1 2NH* This course will enable participants to gain experience and confidence in the identification, to the family level, of British marine Gammarid amphipods. The Gammarid amphipods are a large and diverse group of crustaceans, the identification of which which can be daunting for beginners to macrofaunal taxonomy. There are dozens of amphipod families, and hundreds of amphipod species found in UK waters and their identification requires microscopic examination of very small body parts. This course will guide students through the morphology of amphipods focusing on features used in identification at the family level. The course will use the key text for this field, the 1977 book of British Marine Amphipoda: Gammaridea by Roger J. Lincoln. Many taxonomic papers have been written since clarifying or changing details but this text remains the most comprehensive and accessible key for this group. The workshop will be predominantly lab based with microscope sessions guided by experienced senior taxonomists from the MESL laboratory team and utilising specimens from our in-house reference collection. Becoming familiar with the general morphology of amphipods, and identification to the family level, is a crucial step towards in the development of the skills required to accurately identify these animals to species. * Terebellomorpha and Nephtyidae Identification Workshop**with Dr.Sc. Igor Jirkov ***Booking Now******* *23rd -25th February** Marine Ecological Surveys Ltd, 3 Palace Yard Mews, Bath, BA1 2NH* Dr.Sc .Igor Jirkov, a leading researcher from Moscow State Lomonosov University, will be running a three day workshop focusing on the identification of species belonging to Terebellomorpha and Nephtyidae. User friendly, pictorial identification keys revised by Dr Jirkov will be presented during the workshop and tested using specimens from a variety of sources including our in-house reference collection. Participants are encouraged to bring along their own specimens for advice on identification from Dr Jirkov. *Benthic Taxonomy Summer School *****Booking Now******* *13th -24th June** * *The Marine Life and Environmental Science Resource Centre, Marine Biological Association of the UK, Plymouth*, PL1 2PB The two week Benthic Taxonomy Summer School provides students with hands-on experience working in the marine environment and an introduction to species identification skills. The course will build upon practical sampling and identification skills which many students will have gained during related undergraduate degree courses and provides skill and experience vital to those wishing to pursue a commercial or academic career in Marine Biology. During the first week students have the opportunity to carry out both intertidal and subtidal sampling, using equipment that is routinely used for both commercial and academic collections. Samples collected in the field will be sorted and identified back in the laboratory giving students a taste of the biodiversity found in British seas. The second week of the course focuses on the identification of marine polychaetes and amphipods, two of the most commonly encountered groups of benthic invertebrates. Participants are given the option of attending either or both weeks of the summer school and there will also be the opportunity to learn Seasearch dive survey techniques over the weekend. The summer school will be held at the resource centre at the Marine Biological Association of the UK where students will also have access to the National Marine Biological Library and other MBA resources. Please log on to our website for more detailed information and booking details www.seasurvey.co.uk Best Regards Bryony -- Bryony Pearce BSc (Hons) Research Director Marine Ecological Surveys Ltd 3 Palace Yard Mews Bath BA1 2NH Tel: 01225 442211 E.Mail: bryony@seasurvey.co.uk www.seasurvey.co.uk From dmerrill from k-state.edu Fri Jan 21 15:00:06 2011 From: dmerrill from k-state.edu (Doris Merrill) Date: Fri Jan 21 15:21:15 2011 Subject: [Arthropod] Arthropod Genomics Symposium, Kansas City, June 9-12, 2011 Message-ID: <1859862123.4512484.1295640006145.JavaMail.root@ksu-sfpop-mailstore03> Arthropod Genomics 2011:? Exploring Diversity, Relating Similarity 5th ANNUAL ARTHROPOD GENOMICS SYMPOSIUM June 9 ? 12, 2011, in Kansas City, USA http://www.k-state.edu/agc/symposium.shtml Please plan to attend the 5th Annual Arthropod Genomics Symposium, ?Exploring Diversity, Relating Similarity,? June 9 to 12, 2011, in Kansas City at the Marriott hotel on the beautiful Country Club Plaza.? Registration will open in January. KEYNOTE SPEAKER: Marc A.T. Muskavitch DeLuca Professor of Biology Boston College ?Advancing vector genetics through the power of vector genomics? ? FEATURED SPEAKERS: Gregor Bucher Department of Developmental Biology Georg-August University, G?ttingen, Germany ?iBeetle: Genome wide RNAi screen for embryonic and metamorphic development in Tribolium? ? Owain Edwards Invertebrate Genomics and Evolution CSIRO Ecosystem Sciences Perth, Australia ?DNA methylation and phenotypic plasticity in the pea aphid, Acyrthosiphon pisum? Cassandra Extavour Dept of Organismic and Evolutionary Biology Harvard University ?Overcoming the gene discovery bottleneck for arthropod evo-devo:? Creating de novo developmental transcriptomes? Toni Gabald?n Center for Genomic Regulation (CRG) Barcelona, Spain ?Arthropod genomes as seen through the lens of evolution? Cheryl Y. Hayashi Department of Biology University of California, Riverside ?Spider silks:? Functional and evolutionary insights into high-performance materials? Mary Ann McDowell Biological Sciences University of Notre Dame ?A tale of two sand fly genomes:? Phlebotomus papatasi and Lutzomyia longipalpis? Pedro L. Oliveira Instituto de Bioqu?mica M?dica Programa de Biologia Molecular e Biotecnologia Universidade Federal do Rio de Janeiro and Instituto Nacional de Ci?ncia e Tecnologia em Entomologia Molecular Rio de Janeiro, Brazil ?An insight into the transcriptome of the digestive tract of the blood sucking bug, Rhodnius prolixus? Michael Pfrender Biological Sciences University of Notre Dame ?Genome structure, functional diversification, and Genome X environment interactions in Daphnia? Dorith Rotenberg Plant Pathology Kansas State University ?A genomics-based approach to identify insect molecular components associated with vector competency in Frankliniella occidentalis, the primary thrips vector of Tomato spotted wilt virus? Herv? Seitz Laboratoire de Biologie Mol?culaire Eucaryote CNRS/Universit? Paul-Sabatier Toulouse, France ?Genomics of small RNAs in insects? Alexandra C. Wilson Department of Biology University of Miami ?Genomic insights into nitrogen upgrading and recycling in the aphid [Buchnera] symbiosis? Guojie Zhang Beijing Genome Institute Shenzhen, China ?BGI?s recent activity on insect genomic research? WORKSHOPS A pre-symposium workshop, ?Genome Project 101,? by Scott Cain, OICR, and Dave Clements, Emory University; Thursday afternoon, June 9, 4:00-6:00 p.m. ?Comparative genomics with the generic synteny browser (GBrowse_syn): Configuration and display of various co-linearity data types,? by Sheldon McKay, iPlant, will be presented Saturday morning, June 11. ORGANISM MEETINGS Friday afternoon/evening, June 10 Meet with scientists who are also working with your organism of interest during small group gatherings.? If you are interested in coordinating topics and leading discussions as a group leader, please e-mail dmerrill@ksu.edu .? Additional information will be posted to the conference website as details are finalized. POSTER SESSIONS: There will be two poster sessions.? A few platform presentations will be chosen from submitted poster abstracts. The deadline for submission of poster abstracts is May 18. TENTATIVE SYMPOSIUM PROGRAM ?? Thursday afternoon, June 9 ? Pre-Symposium Workshop ?? Thursday evening, June 9 ? Keynote presentation and welcome reception ?? Friday & Saturday, June 10 and 11 - Platform and Poster sessions ?? Friday afternoon/evening, June 10 ? Organism meetings ?? Saturday morning ? Gbrowse_syn Workshop ?? Sunday morning, June 12 ? Roundtable discussion focusing on I5k with Kevin J. Hackett, USDA, and the ArthropodBase Consortium.? All are invited to attend!? ?? Noon, Sunday, June 12 - Activities will conclude. ROUNDTABLE DISCUSSION:? Participate in a roundtable discussion with the ArthropodBase Consortium regarding the generation of integrated arthropod genome databases and tools for genome projects.? Discussion will focus on I5k, led by Kevin J. Hackett, USDA.? Symposium attendees are encouraged to attend. PRE-CONFERENCE MEETINGS: -International Tribolium Meeting, 6/8 and 6/9. -International Aphid Genomics Consortium, 6/9. REGISTRATION: Registration will be open in January.? Monitor our website, www.k - state.edu/agc/symposium.shtml and watch for the next announcement. VENUE:? The symposium will take place at the Kansas City Marriott on the beautiful Country Club Plaza QUESTIONS:? Contact us at (785) 532-2982 or dmerrill@ksu.edu . Please share this announcement with colleagues and students! SPONSOR:? Center for Genomic Studies on Arthropods Affecting Human, Animal and Plant Health, Kansas State University Susan J. Brown, Professor Director, Center for Genomic Studies on Arthropods Affecting Human, Animal and Plant Health and Robin E. Denell, Distinguished Professor Chair, AGC Symposium Organizing Committee by Doris Merrill, Program Coordinator K-State Arthropod Genomics Center Division of Biology, Kansas State University 116 Ackert Hall, Manhattan, KS? 66506-4901 (785) 532-2982, dmerrill@k-state.edu www.k-state.edu/agc From gilbertd from net.bio.net Sun Jan 23 23:44:48 2011 From: gilbertd from net.bio.net (Don Gilbert) Date: Sun Jan 23 23:47:18 2011 Subject: [Arthropod] RNA-seq transcriptome studies: remove ribosomal rna tip Message-ID: <201101240444.p0O4imH10683@net.bio.net> For those of you contemplating Rna-seq experiments, here is a tip: consider methods to deplete ribosomal RNA before sequencing. In aphid rna-seq data now at NCBI/SRA, the rRNA genes (spread over a mere 300 Kb of poorly assembled scaffolds) account for 50% to over 90% of rnaseq reads, depending on experiment and body tissue. These clog up analyses as well as waste useful experimental effort (i.e. for 1.1 billion aphid reads available, 900 mill are rRNA reads, with 200 million for the rest of transcriptome). I have no experience in the methods involved, but here are examples -- Don Gilbert doi:10.1016/j.ymeth.2009.03.016 RNA-Seq quantitative measurement of expression through massively parallel RNA-sequencing "2.2. rRNA removal One of the principal technical hurdles to overcome with RNA-seq is the fact that the vast majority of RNA (>90%) present in cells consists of ribosomal RNA (rRNA)." http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0000878 "Ribosomal RNA depletion .. Ae. aegypti .. subjected to eukaryotic ribosomal RNA depletion using the RiboMinus Kit (Invitrogen) " From alpapan from gmail.com Mon Jan 24 19:52:10 2011 From: alpapan from gmail.com (Alexie Papanicolaou) Date: Mon Jan 24 20:02:30 2011 Subject: [Arthropod] Re: Arthropod Digest, Vol 10, Issue 5 In-Reply-To: <201101241703.p0OH37p06069@net.bio.net> References: <201101241703.p0OH37p06069@net.bio.net> Message-ID: Yes, indeed. Our values vary, from 18 % to 50 % but my guess it is more relating to total amount of RNA. The species with 18% was within 15-20 % for 8 different libraries/tissues, including examples like head. For another species we had consistently ca 50 % rRNA from 4 libraries. Until a couple of months ago, I was removing redundancy from all the data (using cd-hit-est) and that would remove almost all rDNA. The velvet assemblies looked OK (kmer coverage was even but low) but Brian Haas suggested that for inchworm it is ok to not remove redundancy (inchworm does not use a kmer histogram to filter nodes). for what it is worth, inchworm was better at assembling so an rDNA-flitering step had to be included. my method (which may or may not be optimal) is as follows For every new species: get a 1 M sequences. Align them vs a non-rendundant insect rDNA nucleotide sequence (I use SSAHA despite being slow because it allows % identity cutoffs) e.g. ssaha2 -best 1 -memory 4000 -identity 80 -tags 1 -solexa -score 45 -cmatch 45 -save insecta_rDNA.nr80 Heliconius_all_1.trim24.fsa_dir1000000/Heliconius_all_1.trim24.fsa_2|grep ^ALIGNMENT|grep -o -E 'USI-EA[^ ]+' > Heliconius_all_1.trim24.fsa_dir1000000/Heliconius_all_1.trim24.fsa_2.ssaha get the sequences that match and assemble them separately. BLAST to verify it is all rDNA then you have an rDNA library for that species. For every dataset Use your favourite aligner to pre-process the data and identify rDNA using a species specific rDNA (a fast aligner such as bwa is good) optionally assemble those reads and verify they are all rDNA. Optionally you may not only pick the reads that match an rDNA but also their PE mate (if it is PE) Before all this, I use the fastx_toolkit to quality trim the data (fastq_quality_trimmer -t 19 or -t 24 depending on the difference in file size between the two outputs) ta a On Tue, Jan 25, 2011 at 4:03 AM, wrote: > Send Arthropod mailing list submissions to > ? ? ? ?arthropod@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > ? ? ? ?http://www.bio.net/biomail/listinfo/arthropod > or, via email, send a message with subject or body 'help' to > ? ? ? ?arthropod-request@net.bio.net > > You can reach the person managing the list at > ? ? ? ?arthropod-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Arthropod digest..." > > > Today's Topics: > > ? 1. RNA-seq transcriptome studies: remove ribosomal rna tip > ? ? ?(Don Gilbert) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 23 Jan 2011 23:44:48 -0500 (EST) > From: Don Gilbert > Subject: [Arthropod] RNA-seq transcriptome studies: remove ribosomal > ? ? ? ?rna tip > To: arthropod@magpie.bio.indiana.edu > Message-ID: <201101240444.p0O4imH10683@net.bio.net> > > > > For those of you contemplating Rna-seq experiments, here is a tip: > consider methods to deplete ribosomal RNA before sequencing. > In aphid rna-seq data now at NCBI/SRA, the rRNA genes (spread over a > mere 300 Kb of poorly assembled scaffolds) account for 50% to over > 90% of rnaseq reads, depending on experiment and body tissue. ?These > clog up analyses as well as waste useful experimental effort > (i.e. for 1.1 billion aphid reads available, 900 mill are rRNA reads, > with 200 million for the rest of transcriptome). > > I have no experience in the methods involved, but here are examples > -- Don Gilbert > > doi:10.1016/j.ymeth.2009.03.016 > RNA-Seq quantitative measurement of expression through massively parallel RNA-sequencing > "2.2. rRNA removal > One of the principal technical hurdles to overcome with RNA-seq is the fact that > the vast majority of RNA (>90%) present in cells consists of ribosomal RNA (rRNA)." > > http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0000878 > "Ribosomal RNA depletion .. > Ae. aegypti .. subjected to eukaryotic ribosomal RNA depletion using the RiboMinus Kit (Invitrogen) " > > > > > ------------------------------ > > _______________________________________________ > Arthropod mailing list > Arthropod@net.bio.net > http://www.bio.net/biomail/listinfo/arthropod > > > End of Arthropod Digest, Vol 10, Issue 5 > **************************************** > From yannick.wurm from unil.ch Mon Jan 31 23:19:10 2011 From: yannick.wurm from unil.ch (Yannick Wurm) Date: Tue Feb 1 07:03:47 2011 Subject: [Arthropod] Ant genomes Message-ID: <98FB0A3D-61DB-4B45-9868-D7E65EF06E11@unil.ch> FYI, three ant genomes are out today! S. invicta fire ant : http://www.pnas.org/cgi/doi/10.1073/pnas.1009690108 L. humile argentine : http://www.pnas.org/cgi/doi/10.1073/pnas.1008617108 P. barbatus harvester: http://www.pnas.org/cgi/doi/10.1073/pnas.1007901108 Cheers, yannick ------------------------- Ant Genomes & Evolution http://yannick.poulet.org skype://yannickwurm