HarvEST

Overview of HarvEST

HarvEST was initiated during the EST sequencing era for Barley, Brachypodium, Cassava, Citrus, Coffee, Cowpea, Musa (banana/plantain), Soybean, Rice and Wheat. HarvEST software for Windows can be downloaded from this site (see links below). As of September 2018, no new version of HarvEST will be produced.

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 software was developed at the University of California, Riverside by Steve Wanamaker and Timothy Close. The software can still be downloaded from this website 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 were 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 most functions of HarvEST, no internet connection is required. Key features include: a choice of assemblies, sequence alignment viewing, synteny displays, 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 combinations 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 facilitate connection to NCBI and HarvEST BLAST servers for online searches.

HarvEST:Cowpea (will not be updated)

Version 1.47 of "HarvEST:Cowpea" includes a consensus genetic map derived from five biparental RIL populations genotyed with the Illumina Cowpea iSelect Consortium Array. The software also contains sequence assemblies, map positions and gene content information for over 4,000 BACs from a library of IT97K-499-35 (the "reference genome") as described in Genome resources for climate-resilient cowpea, an essential crop for food security with linkage group numbering modified to optimally match the numbering of common bean chromosomes. BACs are searchable by BAC name or SNP name. Version 1.47 contains a synteny viewer to compare cowpea to common bean, soybean or Arabidopsis. The software also displays 17 EST libraries. 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) were 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 v1.47 contains best BLASTX hits from the common bean genome (v2.1; March 2017), the soybean genome (Wm82.a2.v1; December 2015), UniProt (March 2018) and the Arabidopsis genome (TAIR version 10; November 2010). Development of HarvEST:Cowpea was funded initially by the USDA/CSREES Plant Genome program; updates were supported by funding from the CGIAR Generation Challenge Program, the Feed the Future Innovation Lab for Climate Resilient Cowpea (USAID) and the NSF BREAD program.

HarvEST:Barley (will not be updated)

Version 2.26 of "HarvEST:Barley" is one of several portals to barley genome information provided by members of the International Barley Sequencing Consortium. It contains sequence assemblies, map positions and gene content information for nearly 18,000 BACs of the Morex library of Yu et al. (2000, TAG 101:1093-1099). This includes 15,622 gene-bearing BACs described in Munoz-Amatriain et al. (2015, Plant J DOI: 10.1111/tpj.12959). BACs are searchable by BAC name, SNP name, arm or genetic map position. Version 2.26 includes two barley genetic maps (Munoz-Amatriain et al. 2011, Munoz-Amatrian et al. 2014) and a synteny viewer to compare barley to rice, the wheat D genome or Brachypodium. This version (1.36 GB download, 2.41 GB installed) is also enabled to view the Affymetrix "Barley1" microarray content, including probe set location, probe sequences, and enhanced probe set annotations. This version also 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 2.26 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 (James Hutton 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 (January 2015) and gene models of rice (MSU version 7; October 2011), Arabidopsis (TAIR version 10; November 2010) and Brachypodium (Phytozome Bradi 283 (v2.1)). 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:Citrus (will not be updated)

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:Cassava (will not be updated)

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:Musa (will not be updated)

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 (will not be updated)

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 were supported by the University of California Agricultural Experiment Station.

HarvEST:SoyChip (will not be updated)

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 were supported by the University of California Agricultural Experiment Station.

HarvEST:WheatChip (will not be updated)

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 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 1.20 of HarvEST:Wheat that 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.

Final Releases :

June 24, 2018 HarvEST:Cowpea version 1.47 has the following features:

May 1, 2015 HarvEST:Barley version 2.26 has the following features:

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

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

September 6, 2010 HarvEST:Wheat version 1.20

September 3, 2010 HarvEST:Musa version 1.06

September 3, 2010 HarvEST:SoyChip version 1.10

September 3, 2010 HarvEST:WheatChip version 1.59

September 3, 2010 HarvEST:Coffea version 0.18

September 3, 2010 HarvEST:Brachypodium version 0.54

September 2, 2010 HarvEST:RiceChip version 1.14

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

• 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.
• 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).
• 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.
• Click on a library n Click on a library name to view a detailed description sheet for a library.ame to view a detailed description sheet for a library.
• Click the View Members of Selected Unigene button for a browse-able list of the ESTs in the highlighted unigene.
• Click the Output all Sequences from Selected Unigene button to export the highlighted unigene to a FASTA-formatted text file.
• Click the View/Blast Consensus of Selected Unigene button to perform an NCBI BLASTX-nr search. (This requires an Internet connection.)
• Click the Output the Above Unigene List button to create a FASTA or tab-delimited text file.
• Click the Create a Unigene/Assembly Cross-Reference button to generate a tab-delimited text file.

Select a Different Assembly

• HarvEST contains multiple assemblies. Select this option to switch between them. All other displays are in the context of the selected assembly.

Print Reports

• 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.

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

• Windows 95/98/Me, NT4/2000/XP/Vista/7/8/10 (Windows is REQUIRED)
• 2 GHz or higher processor recommended
• 3 GB free hard disk space is recommended
• 2 GB RAM minimum is recommended
• 1024 x 768 video resolution is REQUIRED
• Internet connection (to use hyperlinks to other databases) is optional, but recommended

Download the Most Recent Version

Click Here To Download HarvEST:Cowpea version 1.47 (6/24/2018) 395 MB download, 623 MB installed.

Click Here To Download HarvEST:Barley version 2.26 (5/1/2015) 1.36 GB download, 2.41 GB installed. This contains six different EST assemblies and BAC sequences with annotations.

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 (9/3/2010) 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:

• Timothy Close, timothy.close@ucr.edu

Copyright Message

HarvEST software copyrights (C) 2001 - 2024 Steve Wanamaker, Timothy Close and the University of California. This web page copyrights (C) 2001 - 2024 Sheila Close, Steve Wanamaker, Timothy Close and the University of California. All rights reserved.