While the IGBB Service Center can perform low-risk, fairly routine biomolecular tasks on a fee-per-service basis, some of your research goals may require (or would most readily be completed with) the help of professionals trained in advanced procedures and/or data analysis techniques. The IGBB research associates, most of whom have Ph.D. degrees and/or many years of practical experience, can be hired to conduct research tasks associated with their specialties. For example, let's say you need an expert in RNA isolation and RNAseq to help you complete a portion of a research project. You could train a student or postdoc to become proficient in these research tasks, but you may not have the experience, time, or money to train someone. Moreover, you may not have the instrumentation you need to do the research correctly. This is where the IGBB can help. Rather than training someone new, you can hire a highly skilled IGBB scientist to perform the research for you. The savings in cost and time is tremendous! The process works like this:
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If you don't have funding in hand, but are working on a grant proposal, you can include the participation of an IGBB expert-for-hire in your proposal budget (note: you must make such agreements with the expert-for-hire through a MyIGBB itemized quote). To discuss a hiring an IGBB expert, please contact one of the IGBB's Research Leads by phone or e-mail.
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Empirical comparison of ab initio repeat finding programs
IGBB Authors:
Surya Saha, Susan Bridges, Zenaida Magbanua, Daniel G. PetersonPUBLICATION YEAR:
2008IMPACT FACTOR:
7.408CITATION COUNT:
258Saha S, Bridges SM, Magbanua ZV, Peterson DG (2008) Empirical comparison of ab initio repeat finding programs.
Nucleic Acids Research 36(7): 2284-2294.
DOI:
10.1093/nar/gkn064EID:
2-s2.0-42449106154PMID: 18287116
DOWNLOAD PDFABSTRACTIdentification of dispersed repetitive elements can be difficult, especially when elements share little or no homology with previously described repeats. Consequently, a growing number of computational tools have been designed to identify repetitive elements in an ab initio manner, i.e. without using prior sequence data. Here we present the results of side-by-side evaluations of six of the most widely used ab initio repeat finding programs. Using sequence from rice chromosome 12, tools were compared with regard to time requirements, ability to find known repeats, utility in identifying potential novel repeats, number and types of repeat elements recognized and compactness of family descriptions. The study reveals profound differences in the utility of the tools with some identifying virtually their entire substrate as repetitive, others making reasonable estimates of repetition, and some missing almost all repeats. Of note, even when tools recognized similar numbers of repeats they often showed marked differences in the nature and number of repeat families identified. Within the context of this comparative study, ReAS and RepeatScout showed the most promise in analysis of sequence reads and assembled genomic regions, respectively. Our results should help biologists identify the program(s), if any, that is best suited for their needs.
Dr. Olga PechanovaSenior Research Associate
PROTEOMICS LEAD
email(662) 325-4570
Pace 115A
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