HarvEST

barley, citrus, cowpea photos

Overview of HarvEST

HarvEST has been 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) most of the EST-related functions of HarvEST can be performed by connecting to www.harvest-web.org. Genetic maps, synteny views and BAC sequence functions are presently available only in the Windows software available from this website.

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 available in other HarvEST software. HarvEST has been developed at the University of California, Riverside by Steve Wanamaker and Timothy Close. The software can be downloaded 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 related to ESTs and BACs. 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:Cowpea

Version 1.33 of "HarvEST:Cowpea" includes a 1091-SNP consensus genetic linkage map (v6) derived from 1117 individuals in 11 mapping populations (Mitchell Lucas and Bao-Lam Huynh, UC Riverside, 2012) 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 v1.33 contains best BLASTX hits from the common bean genome (Phytozome 212, February 2013), 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:Barley

Version 2.02 of "HarvEST:Barley" contains six EST assemblies (21, 25, 31, 32, 35 and 37). 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 #37 includes full length cDNA sequences from Sato and Matsumoto in addition to the sequences present in version #35. Version 2.02 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, 35 or 37 is active. Version 2.02 (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 2.02 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 (August 2013) and gene models of rice (MSU version 7; October 2011), Arabidopsis (TAIR version 10; November 2010) and Brachypodium (Phytozome Brachy 192; February 2012). 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 were funded more recently 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. Map position and gene content information for about 18,000 gene-bearing BACs of Morex library that have been sequenced is also available and exportable from HarvEST:Barley, searchable by BAC name, SNP name, arm or genetic map position. A version of HarvEST:Barley 2.02 containing FASTA files for the sequenced BACs is available on request (contact timothy.close@ucr.edu).

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: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 1.06 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 1.14 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 1.10 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

Version1.59 of "HarvEST:WheatChip" utilizes the same probe set display and annotation functions as HarvEST:Barley, but includes only the assembly that was produced byAffymetrix 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 1.20 of HarvEST:Wheat displays about 101,000 wheat and other Triticeae ESTs produced mainly by a NSF-sponsored wheat project. Version 1.20 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 (will not be updated)

Version 0.54 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 (will not be updated)

Version 0.18 "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.

Most Recent Releases:

February 4, 2014 HarvEST:Barley version 2.02 has the following features:

  • Sequenced Morex BACs anchored to mapped SNP loci, BAC sequence annotations exportable by BAC or SNP name, arm or map position
  • Barley genetic map viewer (active from assemblies 32, 35 and 37) 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
  • EST sequence alignment viewer, sortable by source genotype - to navigate within the CAP3 sequence alignments and find SNP's
  • Batch export of genetic map coordinates, marker names, mapped unigene sequences with annotations
  • Six different EST assemblies
  • Support of the Affymetrix "Barley1" chip: exports probe set annotations, graphical displays of probes on unigenes, other "Search the Barley Chip"functions
  • 444,652 barley ESTs (Sanger), about 1100 other barley sequences from GenBank, 18,519 full length cDNAs of Sato and Matsumoto
  • Best BLASTX of UniProt (August 2013), and genomes of rice (MSU version 7; October 2011), Arabidopsis (TAIR version 10; November 2010) and Brachypodium (Phytozome Brachy 192; February 2012) with hyperlinks
  • Cross-references unigenes between different assemblies
  • 683 MB download, 1.44 GB installed
  • Search by expression pattern
  • Extensive "Output Unigene", BAC sequence information and other export functions (version with BAC sequences available on request)

January 9, 2014 HarvEST:Cowpea version 1.33 has the following features:

  • Cowpea genetic map viewer including 1091 mapped SNP loci, including synteny view of common bean, soybean and Medicago with TIFF export and zoom-in (Windows only; not available through www.harvest-web.org
  • Sequence alignment viewer, sortable by source genotype - to navigate within the CAP3 sequence alignments and view SNP's
  • Two assemblies
  • 183,118 cowpea ESTs
  • Best BLASTX hits from UniProt (Uniref-90; February 2010), the genome of common bean (Phytozome 186; January 2012), soybean (Phytozome Glyma1; December 2008 Arabidopsis (TAIR version 10; November 2010), and Medicago truncatula (IMGAG MT3/5; May 2011), each with hyperlinks
  • 162 MB download, 239 MB installed
  • Search by expression pattern
  • Extensive "Output Unigene" and other export functions

October 10, 2010 HarvEST:Cassava version 1.06 has the following features:

  • Sequence alignment viewer, sortable by source genotype - to navigate within the CAP3 sequence alignments and view SNP's
  • One assembly
  • 58,607 Cassava ESTs
  • Best BLASTX of UniProt (February 2010) and Arabidopsis genome (TAIR version 9; June 2009)
  • 56 MB download, 77 MB installed
  • Search by expression pattern
  • Extensive "Output Unigene" and other export functions

October 28, 2010 HarvEST:Citrus version 1.32 has the following features:

  • 533 MB download, 1004 MB installed
  • 469,618 sequences, including quality values for 95% of ESTs
  • 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)
  • Includes the two "all citrus" assemblies (C37 & C38) used for the Affymetrix Citrus GeneChip®
  • Sequence alignment viewer, sortable by genotype - to navigate within the CAP3 sequence alignments and find SNPs
  • Best BLASTX of UniProt (February 2010), Arabidopsis (TAIR 9; June 2009) and poplar (JGI version Poptr1.1; September 2006) with hyperlinks
  • Arabidopsis and poplar map displays
  • Support of the Affymetrix Citrus GeneChip®: exports probe set annotations, graphical displays of probes on unigenes, other "Search the Citrus Chip" functions
  • Displays Affymetrix Citrus GeneChip® probe positions and other probe details
  • Cross-references unigenes between different assemblies
  • Search by expression pattern
  • Extensive "Output Unigene" and other export functions

September 3, 2010 HarvEST:Musa version 1.06 has the following features:

  • Sequence alignment viewer, sortable by source genotype - to navigate within the CAP3 sequence alignments and view SNP's
  • One assembly
  • 37,772 Musa ESTs
  • Best BLASTX of UniProt (August 2008), rice (MSU version 6; January 2009) Arabidopsis (TAIR 9; June 2009), Brachypodium (Phytozome Bradi 1; May 2009) genomes, with hyperlinks
  • 39 MB download, 56 MB installed
  • Search by expression pattern
  • Extensive "Output Unigene" and other export functions

September 3, 2010 HarvEST:SoyChip version 1.10

September 2, 2010 HarvEST:RiceChip version 1.14

September 3, 2010 HarvEST:WheatChip version 1.59 has the following features:

  • Support of the Affymetrix Wheat chip: exports probe set annotations, graphical displays of probe sets on unigenes, other "Search the Wheat Chip" functions
  • Sequence alignment viewer - to navigate within the CAP3 sequence alignments
  • Contains the assembly created and used by Affymetrix to design the wheat chip
  • Best BLASTX of UniProt (August 2008), rice (MSU version 6; January 2009) Arabidopsis (TAIR 9; June 2009), Brachypodium (Phytozome Bradi 1; May 2009) genomes, with hyperlinks
  • 165 MB download, 435 MB installed
  • "Output Unigene" and other export functions

September 6, 2010 HarvEST:Wheat version 1.20 has the following features:

  • Support of the Affymetrix Wheat chip: exports probe set annotations, graphical displays of probe sets on unigenes, other "Search the Wheat Chip" functions
  • Sequence alignment viewer, sortable by source genotype - to navigate within the CAP3 sequence alignments
  • Four assemblies: two containing 101,107 Triticum Aegilops and Secale ESTs; two containing 91,130 Triticum ESTs
  • Best BLASTX of UniProt (August 2008), rice (MSU version 6; January 2009) Arabidopsis (TAIR 9; June 2009), and Brachypodium (Phytozome Bradi 1; May 2009) genomes, with hyperlinks
  • 162 MB download, 322 MB installed
  • Cross-references unigenes between different assemblies
  • Search by expression pattern
  • Extensive "Output Unigene" and other export functions

September 3, 2010 HarvEST:Coffea version 0.18

September 3, 2010 HarvEST:Brachypodium version 0.54

Screen Shots

Click Here to View HarvEST Screen Shots

Using HarvEST

EST Searches

Search a GeneChip (Barley, Citrus, Rice, Soybean, Wheat)

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.

Search ESTs by Expression Pattern

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.

Search ESTs by best BLAST hit keyword

You may find ESTs in the database by searching by function using keywords.

Search by Genbank#, EST Name, or Unigene#

You may find ESTs by Genbank#, EST name, or HarvEST unigene#. Note: HarvEST unigene numbers change between versions and differ between assemblies.

Results Display

Select a Different Assembly

Print Reports

About HarvEST Assemblies

The assemblies in HarvEST are not identical to clusters created by other programs. The EST unigene numbers are different for each assembly and do not correspond to unigene numbers in any other assembly.The assemblies in the HarvEST versions for Wheat, Rice and Soybean Affymetrix genome arrays 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.

System Recommendations & Requirements

Download the Most Recent Version

Click Here To Download HarvEST:Barley version 2.02 (1/18/2014) 715 MB download, 1.44 GB installed. This contains six different EST assemblies and BAC sequence annotations.

Click Here To Download HarvEST:Cowpea version 1.33 (1/9/2014) 166 MB download, 239 MB installed. This contains two EST assemblies.

Click Here To Download HarvEST:Citrus version 1.32 (10/28/2010) 546 MB download, 1004 MB installed. This contains six different assemblies.

Click Here To Download HarvEST:Cassava version 1.06 (10/6/2010) 58 MB download, 77 MB installed. This contains one assembly.

Click Here To Download HarvEST:Musa version 1.06 (9/3/2010)42 MB download, 56 MB installed. This contains one assembly.

Click Here To Download HarvEST:RiceChip version 1.14 (9/2/2010) 157 MB download, 359 MB installed. This contains one assembly.

Click Here To Download HarvEST:SoyChip version 1.10 (9/3/2010) 136 MB download, 367 MB installed. This contains one assembly.

Click Here To DownloadHarvEST:Wheat version 1.20 (9/6/2010) 169 MB download, 322 MB installed. This contains four different assemblies.

Click Here To Download HarvEST:WheatChip version 1.59 (9/3/2010) 172 MB download, 435 MB installed. This contains one assembly.

Click Here To DownloadHarvEST:Brachypodium version 0.54 (9/30/2010) 28 MB download, 30 MB installed. This contains two assemblies.

Click Here To Download HarvEST:Coffee version 0.18 (9/3/2010) 62 MB download, 83 MB installed. This contains two assemblies.

To Install

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.

To Upgrade to a New Version

Un-install the previous version through Windows (see below), then install the new version.

To Un-Install

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.

HarvEST License Agreement

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 intend to make your analyses of data in this software publicly available.
  2. You may re-distribute HarvEST software as long as:
    1. You do not charge for it.
    2. You do not alter it in any way.
    3. 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:

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