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Overview of HarvEST
HarvEST is now available for the following organisms: Barley, Brachypodium, Cassava, Citrus, Coffee, Cowpea, Musa (banana/plantain), Soybean, Rice, Wheat. HarvEST software for Windows can be downloaded from this site (see links below). For online functionality (slower than Windows, not all functions are available online yet) many functions of HarvEST can be used by connecting to www.harvest-web.org.
HarvEST originated as EST database-viewing software in support of gene function analyses and oligonucleotide design, then grew to support activities including microarray content design, SNP identification, genotyping platform design, comparative genomics and the coupling of physical and genetic maps. HarvEST:Barley and HarvEST:Cowpea are presently the most fully enabled of the HarvEST software suite, as they provide on-the-fly synteny viewing and image export capabilities not yet available in other HarvEST software. HarvEST has been developed at the University of California, Riverside by Steve Wanamaker and Timothy Close. The software is downloadable from this web site as installation files (see postings below) that allow HarvEST to run on any PC that uses Windows and meets the minimum hardware configuration (including Macintosh with a Windows emulator). Unless otherwise stated, all EST sequences have been quality trimmed, cleaned of vector, and assembled using CAP3 with quality values (special thanks to Xiaoqiu Huang for enhanced versions of CAP3). Exceptions are versions of HarvEST containing assemblies received from Affymetrix that were the basis of Affymetrix rice, soybean and wheat genome arrays. HarvEST includes an ACE file viewer that allows the user to examine the sequence alignment and readily determine where individual sequences reliably deviate from a consensus sequence, including SNPs. For key features of HarvEST, no Internet connection is required. Key features include: a choice of assemblies, sequence alignment viewing, synteny displays (available only in Windows versions), archived BLAST hit information, unigene export, Boolean searching with user-defined quantitative settings, and various other searching, reporting and export functions. The unigene export feature can be applied to entire assemblies, individual libraries, or any combination of libraries. For Boolean searches, a user sets parameters according to their interest. For example, the choice could be genes associated with a particular stress (e.g. low temperature, heat, drought, aluminum, nitrogen deprivation), developmental stage (e.g. malted seed, pre-anthesis spike, mature fruit), or tissue (e.g. endosperm, pericarp, embryo sac, rachis, root tip, rind). The user also decides what percentage representation is relevant. Once the choices have been made, the search is executed locally and a browsable output is displayed. The output can be viewed on-screen or exported as summary tables or sequence files. HarvEST also contains hyperlinks to other sequence databases and facilitates connection to NCBI and the HarvEST BLAST servers for online searches.
Please check this site periodically for new versions. Subsequent versions will respond to user feedback and contain updated information and new functions, including more web-operability. If you would like to be automatically notified of new versions, please send a message asking that you are placed on a notification list.
HarvEST:Barley
Version 1.83 of "HarvEST:Barley" contains six assemblies (21, 25, 31, 32, 35 and 36). Assemblies #21 and #25 were the basis of the "Barley1" microarray produced by Affymetrix as part of the USDA-IFAFS project, "An Integrated Physical and Expression Map of Barley for Triticeae Improvement" (Close et al. 2004. Plant Physiology 134: 960-968). Assembly #31 was used for overgo probe design to screen a Morex BAC library for gene-bearing clones in the NSF Plant Genome Research Program project, "Coupling EST Sequences and BAC Resources to Access the Barley Genome". Assemblies #32 and #35 were the main sources of SNPs for Illumina oligonucleotide pool assays developed initially for the same NSF Plant Genome Research project and subsequently the USDA-CSREES Barley Coordinated Agricultural Project (BarleyCAP) (Close et al. 2009. BMC Genomics 10:582). Assembly #36 combines short-read transcriptome consensus sequences from Morex barley, produced in the USDA-AFRI-NIFA project "Advancing the Barley Genome", with other sequences used for assembly #35. Version 1.83 includes a barley genetic map including 2994 SNP loci (Munoz, Moscou et al. 2011. The Plant Genome, submitted) and a synteny viewer to compare barley to rice or Brachypodium (Windows only; map viewer not available through www.harvest-web.org); the map viewer is functional only when assembly #32 or #35 is active. Version 1.83 (674 MB download, 1.20 GB installed) is enabled to view the Affymetrix "Barley1" microarray content, including probe set location, probe sequences, and enhanced probe set annotations. Version 1.83 contains barley EST data sets of more than 30,000 each from USDA-funded projects in the US (Rod Wing et al.), IPK Gatersleben (Andreas Graner et al.), Okayama University and the National Institute of Genetics (Kaz Sato et al.), Scottish Crop Research Institute (Robbie Waugh et al.), and University of Helsinki (Alan Schulman et al.), as well as smaller (less than 3,000 each) datasets of barley ESTs, whole cDNAs and genomics sequences from several other contributors. HarvEST:Barley contains best BLASTX hits from UniProt (February 2010) and gene models of rice (MSU version 6; January 2009), Arabidopsis (TAIR version 10; November 2010) and Brachypodium (Phytozome Bradi 1; May 2009). Development of HarvEST:Barley was initially funded by the USDA/CSREES Plant Genome program and then the NSF Plant Genome Research Program; updates and maintenance are currently funded by the USDA-AFRI-NIFA program, in the project "Advancing the Barley Genome". HarvEST:Barley is one of several portals to barley genome information provided by members of the International Barley Sequencing Consortium.
Click here to see more about the relationship of HarvEST:Barley and the Affymetrix Barley1 GeneChip including a powerful probe set annotation tool available in HarvEST:Barley.
HarvEST:Cassava
Version 1.06 of "HarvEST:Cassava" displays EST sequences from 5 cDNA libraries from Manihot esculenta. All sequences were derived from trace files received by T Close and S Wanamaker at UC Riverside from German Plata (International Center for Tropical Agriculture; downloaded from NCBI TraceDB; 34,955 ESTs), James Anderson (USDA-ARS, Fargo, North Dakota, USA; 18,633 ESTs) or Sarah Hearne (International Institute of Tropical Agriculture; 5019 ESTs). HarvEST:Cassava v1.06 contains best BLASTX hits from UniProt (February 2010) and Arabidopsis genome gene models (TAIR version 9; June 2009). Development of HarvEST:Cassava was funded by the International Institute of Tropical Agriculture.
HarvEST:Cowpea
Version 1.27 of "HarvEST:Cowpea" includes a 1107-SNP consensus genetic linkage map derived from 1293 individuals in 13 mapping populations (Lucas, Diop et al., 2011) and displays 17 EST libraries from Vigna unguiculata. ESTs sequenced at the US Department of Energy Joint Genome Institute (141,050 ESTs), the J Craig Venter Institute (41,505 ESTs) and the University of California Riverside (488 ESTs) have been derived from chromatograms. These ESTs, from 12 libraries produced at UC Riverside and 2 at the International Institute for Tropical Agriculture, retain their Phred quality values and can be viewed more extensively than the remaining 75 ESTs, which were downloaded from the GenBank dbEST database as flat files. HarvEST:Cowpea v1.27 contains best BLASTX hits from the soybean genome (Phytozome Glyma1; December 2008), UniProt (February 2010), the Arabidopsis genome (TAIR version 10; November 2010), and the Medicago truncatula genome (IMGAG Mt3.5; May 2011). Initial development of HarvEST:Cowpea was funded by the USDA/CSREES Plant Genome program; updates have been supported by the CGIAR Generation Challenge Program.
HarvEST:Citrus
Version 1.32 of "HarvEST:Citrus" is a major upgrade from prior versions, now displaying 141 libraries and 469,618 ESTs from Citrus and Poncirus. ~95% of the EST sequences have been derived from chromatograms using the full HarvEST pipeline. These ESTs retain their phred quality values and therefore can be viewed more extensively than the remaining ~5% of sequences. HarvEST:Citrus contains best BLASTX hits from UniProt (February 2010), the Arabidopsis genome (TAIR version 9; June 2009) and the poplar genome (Phytozome version Poptr1.1; September 2006). Initial development of HarvEST:Citrus was supported by the USDA/CSREES Plant Genome program; subsequent development was supported by the California Citrus Research Board, the University of California Discovery Grant Program and presently the Florida Citrus Production Research Advisory Council.
HarvEST:Musa
Version 1.04 of "HarvEST:Musa" displays EST sequences from 13 cDNA libraries from Musa acuminata, Musa balbisiana and related species. All sequences were derived from trace files received by T Close and S Wanamaker at UC Riverside from the Global Musa Genomics Consortium (35,718 ESTs) or the J Craig Venter Institute (2,054 ESTs). HarvEST:Musa contains best BLASTX hits from UniProt (August 2008), the annotated rice (MSU version 6; January 2009) and Arabidopsis (TAIR version 9; June 2009) genomes, and Brachypodium (Phytozome Bradi 1; May 2009) gene models. Development of HarvEST:Musa was funded by the International Institute of Tropical Agriculture.
HarvEST:RiceChip
Version 1.12 of "HarvEST:RiceChip" utilizes the same probe set display and annotation functions as HarvEST:Barley, but includes only the assembly that was produced by Affymetrix for the rice GeneChip®. HarvEST:RiceChip contains best BLASTX hits from UniProt (August 2008), BLASTN from rice (MSU version 6; January 2009), and BLASTX from Arabidopsis (TAIR version 9; June 2009) and Brachypodium (Phytozome Bradi 1; May 2009) gene models. Development of HarvEST:Rice was funded initially by the USDA/CSREES Plant Genome program; updates are supported by the University of California Agricultural Experiment Station.
HarvEST:SoyChip
Version 1.08 of "HarvEST:SoyChip" utilizes the same probe set display and annotation functions as HarvEST:Barley, but includes only the assembly that was produced by Affymetrix for the soybean GeneChip® content design. HarvEST:SoyChip contains best BLASTX hits from UniProt (August 2008), the soybean genome (Phytozome Glyma1; December 2008), the Arabidopsis genome (TAIR version 9; June 2009) and the Medicago truncatula genome (IMGAG MT2; May 2008). Initial development of HarvEST:SoyChip was supported by the USDA/CSREES Plant Genome program; updates are supported by the University of California Agricultural Experiment Station.
HarvEST:WheatChip
Version 1.57 of "HarvEST:WheatChip" utilizes the same probe set display and annotation functions as HarvEST:Barley, but includes only the assembly that was produced by Affymetrix for the wheat GeneChip® content design. HarvEST:WheatChip contains best BLASTX hits from UniProt (August 2008), the rice genome (MSU version 6; January 2009), and the Arabidopsis (TAIR version 9; June 2009) and Brachypodium (Phytozome Bradi 1; May 2009) gene models. HarvEST:Wheat is a somewhat related software; Version 1.18 of HarvEST:Wheat displays about 101,000 wheat and other Triticeae ESTs produced mainly by a NSF-sponsored wheat project. Version 1.18 of HarvEST:Wheat contains four assemblies. Initial development of HarvEST:WheatChip and HarvEST:Wheat was funded by the USDA/CSREES Plant Genome program; updates are supported by the University of California Agricultural Experiment Station.
HarvEST:Brachypodium
Version 0.53 of "HarvEST:Brachypodium" displays 6 libraries from Brachypodium distachyon. All sequences were downloaded from the GenBank dbEST database by Steve Wanamaker at UC Riverside. HarvEST:Brachypodium contains best BLASTX hits from UniProt (January 2007) and the rice (TIGR version 5; February 2007) and Arabidopsis (TAIR version 7; April 2007) genomes. Initial development of HarvEST:Brachypodium was funded by the USDA/CSREES Plant Genome program.
HarvEST:Coffea
Version 0.16 of "HarvEST:Coffea" displays 12 libraries from Coffea arabica, Coffea canephora or an interspecies hybrid. All sequences with quality values were received by Steve Wanamaker at UC Riverside from the Tanksley lab at Cornell University or downloaded as flat files from the GenBank dbEST database. HarvEST:Coffea contains best BLASTX hits from UniProt (August 2008), and rice (MSU version 6; January 2009), Arabidopsis (TAIR version 9; June 2009) and Brachypodium (Phytozome Bradi 1; May 2009) gene models. Initial development of HarvEST:Coffea was funded by the USDA/CSREES Plant Genome program.
We can apply the copyrighted HarvEST software to EST assemblies from any organism. Click here to see the file requirements if you have an interest in working with us to do this.
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Larger assemblies for citrus and others |
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Links to BAC clones and contigs for barley and cowpea |
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Barley genetic map viewer (active from assemblies #32 and #35) including 2994 mapped SNP loci, including rice and Brachypodium synteny view with TIFF export and zoom-in (Windows only; not available through www.harvest-web.org) |
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Morex BACs anchored to more than 50% of mapped SNP loci |
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Sequence alignment viewer, sortable by source genotype - to navigate within the CAP3 sequence alignments and find SNP's |
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Batch export of genetic map coordinates, marker names, mapped unigene sequences with annotations |
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Six different assemblies |
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Support of the Affymetrix "Barley1" chip: exports probe set annotations, graphical displays of probes on unigenes, other "Search the Barley Chip" functions |
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444,652 barley ESTs (Sanger), about 1100 other barley sequences from GenBank, deep transcriptome short-read assembly |
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Best BLASTX of UniProt (February 2010), rice (MSU version 6; January 2009), Arabidopsis (TAIR version 10; November 2010) and Brachypodium (Phytozome Bradi 1; May 2009) genomes, with hyperlinks |
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Cross-references unigenes between different assemblies |
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674 MB download, 1.20 GB installed |
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Search by expression pattern |
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Extensive "Output Unigene" and other export functions |
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Sequence alignment viewer, sortable by source genotype - to navigate within the CAP3 sequence alignments and view SNP's |
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One assembly |
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58,607 Cassava ESTs |
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Best BLASTX of UniProt (February 2010) and Arabidopsis genome (TAIR version 9; June 2009). |
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56 MB download, 77 MB installed |
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Search by expression pattern |
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Extensive "Output Unigene" and other export functions |
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Cowpea genetic map viewer including 1107 mapped SNP loci, including soybean and Medicago synteny view with TIFF export and zoom-in (Windows only; not available through www.harvest-web.org) |
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Sequence alignment viewer, sortable by source genotype - to navigate within the CAP3 sequence alignments and view SNP's |
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Two assemblies |
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183,118 cowpea ESTs |
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Best BLASTX hits from UniProt (Uniraf-90; February 2010), the soybean genome (Phytozome Glyma1; December 2008), Arabidopsis (TAIR version 10; November 2010), and the Medicago truncatula genome (IMGAG MT3/5; May 2011), each with hyperlinks |
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160 MB download, 279 MB installed |
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Search by expression pattern |
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Extensive "Output Unigene" and other export functions |
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533 MB download, 1004 MB installed |
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469,618 sequences, including quality values for 95% of ESTs |
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Six assemblies in total: three combining all citrus species (assemblies C37, C38 and C52), one with only Poncirus trifoliata (assembly C53; 38,290 ESTs), one with only Citrus sinensis (assembly C54; 228,199 ESTs), one with only Citrus reticulata (assembly C55; 138,098 ESTs). |
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Includes the two "all citrus" assemblies (C37 & C38) used for the Affymetrix Citrus GeneChip® |
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Sequence alignment viewer, sortable by genotype - to navigate within the CAP3 sequence alignments and find SNPs |
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Best BLASTX of UniProt (February 2010), Arabidopsis (TAIR 9; June 2009) and poplar (JGI version Poptr1.1; September 2006) with hyperlinks |
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Arabidopsis and poplar map displays |
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Support of the Affymetrix Citrus GeneChip®: exports probe set annotations, graphical displays of probes on unigenes, other "Search the Citrus Chip" functions |
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Displays Affymetrix Citrus GeneChip® probe positions and other probe details |
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Cross-references unigenes between different assemblies |
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Search by expression pattern |
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Extensive "Output Unigene" and other export functions |
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Sequence alignment viewer, sortable by source genotype - to navigate within the CAP3 sequence alignments and view SNP's |
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One assembly |
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37,772 Musa ESTs |
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Best BLASTX of UniProt (August 2008), rice (MSU version 6; January 2009), Arabidopsis (TAIR version 9; June 2009), Brachypodium (Phytozome Bradi 1; May 2009) genomes, with hyperlinks |
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39 MB download, 56 MB installed |
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Search by expression pattern |
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Extensive "Output Unigene" and other export functions |
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Support of the Affymetrix Wheat chip: exports probe set annotations, graphical displays of probe sets on unigenes, other "Search the Wheat Chip" functions |
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Sequence alignment viewer - to navigate within the CAP3 sequence alignments |
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Contains the assembly created and used by Affymetrix to design the wheat chip |
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Best BLASTX of UniProt (August 2008), rice (MSU version 6; January 2009), Arabidopsis (TAIR version 9; June 2009) and Brachypodium (Phytozome Bradi 1; May 2009) genomes, with hyperlinks |
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165 MB download, 435 MB installed |
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"Output Unigene" and other export functions |
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Support of the Affymetrix Wheat chip: exports probe set annotations, graphical displays of probe sets on unigenes, other "Search the Wheat Chip" functions |
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Sequence alignment viewer, sortable by source genotype - to navigate within the CAP3 sequence alignments |
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Four assemblies: two containing 101,107 Triticum, Aegilops and Secale ESTs; two containing 91,130 Triticum ESTs |
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Best BLASTX of UniProt (August 2008), rice (MSU version 6; January 2009), Arabidopsis (TAIR version 9; June 2009) and Brachypodium (Phytozome Bradi 1; May 2009) genomes, with hyperlinks |
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162 MB download, 322 MB installed |
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Cross-references unigenes between different assemblies |
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Search by expression pattern |
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Extensive "Output Unigene" and other export functions |
Click Here to View HarvEST Screen Shots
You may input single probeset names or browse to a list of probe set names. You may output annotations or view the details of the unigenes. To generate annotations you may decide how many probes in a probe set must match an annotated unigene to absorb the annotation. The highest blastx score from any unigene touched by the probe set is reported.
Select libraries in which you wish to see EST’s by entering, in the Min % field above the "Include" column, a minimum threshold percentage (example 0.2%), and putting a check mark next to each desired library.
Select the libraries from which you wish to exclude EST’s by entering, in the Max % field above the "exclude column", a maximum threshold percentage (example 0.04%), and putting a check mark next to each of those libraries.
You may find ESTs in the database by searching by function using keywords.
You may find ESTs by Genbank #, EST name, or HarvEST unigene #. Note: HarvEST unigene numbers change between versions and differ between assemblies.
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The unigene(s) selected through one of the above searches are shown on the left side. The right side has alternative views, controlled by selections on the upper right. The "Distribution Among Libraries" view displays where each member of the unigene was found within the libraries. For each library, the number of unigene members, percentage of library, and a bar graph of the percentage of library are shown. The "Alignment" view shows the position and orientation of each EST within each CAP3 contig. The "Sequence Alignment" view shows the full sequence information, including colorized representation of phred quality values and positions of deviation from the consensus sequence. | |
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The best BLASTX hit against the translated NCBI nr database for the highest-scoring sequence in the selected contig is shown at the bottom left, and against the TIGR annotated rice (IRGSP) and/or Arabidopsis genome in the adjacent window(s). | |
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Scrolling
through the list of unigenes causes the display of libraries on the right to
change to reflect the distribution of the each unigene
that is highlighted. | |
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Click on a library name to view a detailed description sheet for a library. | |
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Click the View Members of Selected Unigene button for a browse-able list of the ESTs in the highlighted unigene. | |
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Click the
Output all Sequences from Selected Unigene button to export the
highlighted unigene to a FASTA-formatted text file. | |
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Click the
View/Blast Consensus of Selected Unigene button to perform an NCBI
BLASTX-nr search. (This requires an Internet connection.) | |
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Click the Output the Above Unigene List button to create a FASTA or tab-delimited text file. |
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Click the Create a Unigene/Assembly Cross-Reference button to generate a tab-delimited text file. |
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HarvEST contains multiple assemblies. Select this option to switch between them. All other displays are in the context of the selected assembly. |
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The "Library Summary" shows the libraries are in the assembly and how many clones, contigs, contigs unique to the library, and singletons for each library. The "Orientation Calls by Library Report" shows the number of forward and reverse orientation reads from each library. Orientations are determined by a combination of sequencing primer information, presence of polyT or polyA, and best BLASTX orientation. The "Print a Summary by Source" lists the number of ESTs from each person, lab, or group. These numbers are generally a little higher than reported elsewhere in HarvEST since some types of hidden ESTs that are in an intermediate processing stage may be counted. |
The assemblies in HarvEST are not identical to clusters created by other programs. The unigene numbers are different for each assembly and do not correspond to unigene numbers in any other assembly or database. The assemblies in the HarvEST:Affymetrix versions for Wheat, Rice and Soybean were produced by Affymetrix and have been included in HarvEST software with permission of Affymetrix. HarvEST:Barley assembly #21 was the source of barley content for the Affymetrix barley genome array. HarvEST:Citrus assemblies #37 and #38 were the sources of citrus content for the Affymetrix citrus genome array.
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Windows 95/98/Me, NT4/2000/XP/Vista/7 (Windows is REQUIRED; for online function go to www.harvest-web.org) |
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1.3 GHz or higher processor recommended |
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2 GB free hard disk space is REQUIRED for HarvEST:Barley |
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1
GB RAM minimum recommended |
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1024 x 768
video resolution is REQUIRED |
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Internet connection (to use hyperlinks to other databases from HarvEST - optional, but nice) |
Click Here To Download HarvEST:Barley version 1.83 (9/28/2011) 674 MB download, 1.20 GB installed. This contains six different assemblies. See License Agreement (below) and System Requirements (above).
Click Here To Download HarvEST:Brachypodium version 0.53 (6/11/2009) 21 MB download, 30 MB installed. This contains two assemblies. See License Agreement (below) and System Requirements (above).
Click Here To Download HarvEST:Cassava version 1.06 (9/15/2011) 56 MB download, 77 MB installed. This contains one assembly. See License Agreement (below) and System Requirements (above).
Click Here To Download HarvEST:Citrus version 1.32 (10/28/2010) 533 MB download, 1004 MB installed. This contains six different assemblies. See License Agreement (below) and System Requirements (above).
Click Here To Download HarvEST:Coffee version 0.16 (11/9/2009) 59 MB download, 83 MB installed. This contains two assemblies. See License Agreement (below) and System Requirements (above).
Click Here To Download HarvEST:Cowpea version 1.27 (8/19/2011) 164 MB download, 279 MB installed. This contains two assemblies. See License Agreement (below) and System Requirements (above).
Click Here To Download HarvEST:Musa version 1.04 (11/9/2009) 39 MB download, 56 MB installed. This contains one assembly. See License Agreement (below) and System Requirements (above).
Click Here To Download HarvEST:RiceChip version 1.12 (11/9/2009) 152 MB download, 359 MB installed. This contains one assembly. See License Agreement (below) and System Requirements (above).
Click Here To Download HarvEST:SoyChip version 1.08 (11/9/2009) 131 MB download, 367 MB installed. This contains one assembly. See License Agreement (below) and System Requirements (above).
Click Here To Download HarvEST:Wheat version 1.18 (11/9/2009) 162 MB download, 322 MB installed. This contains four different assemblies. See License Agreement (below) and System Requirements (above).
Click Here To Download HarvEST:WheatChip version 1.57 (11/9/2009) 165 MB download, 435 MB installed. This contains one assembly. See License Agreement (below) and System Requirements (above).
Download the H*.exe file to a local hard drive. Double click the H*.exe file to launch the Windows installer. The installation directory defaults to a sub-directory off of C:\HarvEST. You may select an alternate location if you wish. The different HarvEST programs can be installed without conflicting with each other. The Visual FoxPro runtime libraries will be installed and the executable and data files will be de-compressed to the installation directory.
Un-install the previous version through Windows (see below), then install the new version.
Go to Control Panel, Add/Remove programs, Click on HarvEST, click Remove. Any residual directory, contents or desktop icon can then be manually deleted. A separate uninstallation through Windows must be performed for each HarvEST software.
To
receive and use this program you must agree to the following conditions:
1. This software is available free of charge for academic purposes. Contact us for a price quote if you do not make your data publicly available.
2. You may re-distribute HarvEST software as long as:
a. You do not charge for it.
b. You do not alter it in any
way.
c. You do not include it as part of software that you charge for.
3. You agree to give us feedback concerning program performance, ease of use, the utility of various features, and any errors found.
Contacts for questions, bug reports, suggestions:
Steve
Wanamaker, steve.wanamaker@ucr.edu
