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  • Soybean BAC Library Alternate Names
    reference list of the official name and the various deprecated alternates In the future all BAC libraries should conform to the GM nomenclature described below GM WBa0103H02 where GM genus species abbreviation in this case Glycine max W 1 char abbreviation for the cultivar in this case Williams82 B library type in this case BAC a library designator in this case the lower case a signifies that this is the

    Original URL path: http://soybase.org/BAC_name_crossref.php (2016-04-30)
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  • Chromosome Number to Linkage Group Assignments
    et al 2003 Assignment of molecular linkage groups to soybean chromosomes by primary trisomics Theor Appl Genet 107 745 750 and citations therein The remaining 9 were given chromosome numbers in decreasing order of linkage group genetic length Chromosome Number Linkage Group Length cM Criteria 1 D1a 98 41 previously assigned 2 D1b 140 63 genetic length 3 N 99 51 previously assigned 4 C1 112 32 previously assigned 5

    Original URL path: http://soybase.org/LG2Xsome.php (2016-04-30)
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  • SoyBase Sequence Map Resources Page
    develop the following nomenclature conventions Gene Model Version Glyma 1 1 to Glyma 2 0 Correspondence Lookup Use this quick and easy tool to look up the name correspondences between the Wm82 a1 v1 1 and Wm82 a2 v1 annotations Genome assembly nomenclature Glyma Wm82 a1 the original JGI assembly previously known as Glyma1 01 aka assembly 1 Glyma Wm82 a2 assembly 2 As other cultivars are sequenced the genotype prefix Wm82 will be changed as needed e g Glyma Forr a1 Similarly a G soja genome assembly would be Glyso PI25345 a1 Gene annotation nomenclature An annotation version number is appended to the assembly name Glyma Wm82 a1 v1 initial JGI annotation Glyma Wm82 a1 v1 1 the JGI 1 1 annotation Glyma Wm82 a2 v1 the current annotation Gene model nomenclature Since many papers have been published for the assembly 1 annotation 1 or 1 1 the names will remain unchanged Glyma10g34560 no change from previous usage Genes in the 2nd and future JGI assemblies and annotations are distinguished by a period after Glyma and 6 rather than 5 digits after the g Glyma 01g123450 1 Wm82 a2 v1 Note the 1 after the locus name is used to distinguish a transcript or splice variant Glyso 01g112340 1 PI125345 a1 v1 Use this quick and easy tool to look up the name correspondences between the Wm82 a1 v1 1 and Wm82 a2 v1 annotations An example A locus in Williams 82 assembly version 2 annotation version 1 with 2 transcripts locus i e gene model identifier Glyma 01g123499 Wm82 a2 v1 locus name Glyma 01g123499 transcript identifiers Glyma 01g123499 1 Wm82 a2 v1 and Glyma 01g123499 2 Wm82 a2 v1 transcript names Glyma 01g123499 1 and Glyma 01g123499 2 In publications the full locus identifier can be used

    Original URL path: http://soybase.org/aboutgenomenomenclature.php (2016-04-30)
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  • SoyBase.org - Gene Model Correspondence Lookup
    defaults used at SoyBase However one consequence of this is that the new gene models are sometimes substantially different from the cognates in previous annotations To differentiate the various genome assemblies and annotations a new nomenclature has been adopted and the genes annotated to the new genome assembly have been named using this style In short the new nomenclature makes these changes A dot i e period character now separates the GenusSpecies prefix from the rest of the name The number of digits after the g is now 6 and steps between genes are now 100 Assembly and annotation info are now included in ID names For example for Williams 82 assembly version 2 annotation version 1 Locus Glyma 01g000100 Locus ID Glyma 01g000100 Wm82 a2 v1 Transcript Glyma 01g000100 1 Transcript ID Glyma 01g000100 1 Wm82 a2 v1 Although the names have changed to reflect the new nomenclature 48606 of the 56044 Wm82 a2 v1 gene models can be unambiguously matched to those in the previous Glyma1 1 annotation This page provides a tool that accepts a list of gene names and returns a table of correspondences as provided by JGI To use this tool paste a list of

    Original URL path: http://soybase.org/correspondence/index.php (2016-04-30)
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  • SoyMap II: About
    from the project and to the twelve focus regions in the project which are being sequenced and studied in detail The NSF project SoyMap II also give the opportunity for undergraduate students to conduct research in plant genomics molecular biology bioinformatics and computer science during the SoyMap Summer Research Program 2015 Seven wild perennial Glycine species were included in the SoyMap II project because of interesting traits G tomentella was included because it has successfully crossed with G max Newell et al 1987 G canescens was included due to reported resistance to various pathogens Hartman et al 2000 G stenophita and G syndetika were chosen because they have each contributed genomes to recent perennial polyploids Doyle et al 2004 This project is evaluating genomic diversity by sequencing twelve half megabase genomic regions selected to include many traits with potential utility for soybean improvement Click here to view more information about the seven wild perennial Glycine species Data for this project Click here to view all publicly available data sequence alignment statistics and methods Click here to explore Glycine species specific data Regions of Interest assembly v2 0 Region Pair Nickname Region Interest chrA start end chrB start end SCN1 SCN2 nematode resistance Gm18 1 666 460 2 000 762 Gm11 32 603 866 32 940 400 seed protein seed composition Gm20 33 343 658 33 641 332 Gm10 37 621 924 37 921 195 LG E A2 structural traits Gm15 50 347 696 50 653 388 Gm08 12 128 367 12 550 870 Dt1 Dt2 morphological Gm19 45 033 356 50 013 023 Gm03 40 372 379 40 668 152 Rpp1 Rpp2 ASR resistance Gm18 51 379 854 51 682 831 Gm09 48 099 948 48 398 414 isoflavone synthase seed composition Gm07 37 011 571 37 320 614 Gm13

    Original URL path: http://soybase.org/soymap2/ (2016-04-30)
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  • SoySNP50K iSelect BeadChip - SoyBase
    reduced representation libraries from several soybean accessions which included six cultivated and two wild soybean G soja Sieb et Zucc genotypes These reads were mapped to the soybean whole genome sequence and 209 903 SNPs were identified After applying several filters a total of 146 161 SNPs were determined to be candidates for Illumina Infinium II BeadChip design To equalize the distance between selected SNPs increase assay success rate and minimize the number of SNPs with low minor allele frequency an iteration algorithm based on a selection index was developed and used to select 60 800 SNPs for Infinium BeadChip design Of the 60 800 SNPs 50 701 were targeted to euchromatic regions and 10 000 to heterochromatic regions of the 20 soybean chromosomes In addition 99 SNPs were targeted to unanchored sequence scaffolds Of the 60 800 SNPs a total of 52 041 passed Illumina s manufacturing phase to produce the SoySNP50K iSelect BeadChip Validation of the SoySNP50K chip with 96 landrace genotypes 96 elite cultivars and 96 wild soybean accessions showed that 47 337 SNPs were polymorphic and generated successful SNP allele calls In addition 40 841 of the 47 337 SNPs 86 had minor allele frequencies 10 among the landraces elite cultivars and the wild soybean accessions Search SoyBase for a specific SoySNP50K SNP Search Examples ss715578909 or BARC 1 01 Gm01 29091115 A G Note Searches covering the original BARC SNPs can be done on this page The dbSNP ID e g ss715587030 is the official name of the SoySNP50K SNPs and should always be used in publications The SoySNP50K Nomenclature Conversion Tool can be used to convert a list of deprecated names into their dbSNP IDs View SoySNP50K SNPs in SoyBase Genome Browser Select a Chromosome Gm01 Gm02 Gm03 Gm04 Gm05 Gm06 Gm07 Gm08 Gm09

    Original URL path: http://soybase.org/snps/index.php (2016-04-30)
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  • BARCSOYSSR Potential SSR Search Page
    BARCSOYSSR Potential SSR Database The BARCSOYSSR Potential SSR Database search page allows users to retrieve data about the Wm82 potential SSRs identified by Qijian Song and Perry Cregan Crop Sci 2010 50 1950 1960 Currently only the entire dataset including primer sequences for PCR amplification is available for download as an MS Excel file In the near future there will be a search feature for downloading potential SSR data for

    Original URL path: http://soybase.org/BARCSOYSSR/index.php (2016-04-30)
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  • SoyBase.org
    significant increase in gene expression between two tissues and the lower triangle as the genes that show a significant decrease in gene expression between the same two tissues This is the same as saying for each cell the tissues across the bottom will have this many genes that have a significant increase in gene expression than the tissues on the left The table below is color coded from white to green to purple based on the number of genes in each cell Clicking on the cell will result in a downloadable list of genes for further exploration One application of this table is to explore the differential gene expression between two developmental time points in a tissue of interest to gain insight into the gene functions and thereby the biological processes that occur during particular stages of development Tissue by Tissue Comparison young leaf 0 10262 5603 5721 5432 2119 3446 2886 3293 1804 3785 2232 11588 6958 flower 7298 0 5278 5191 4038 1389 2841 2474 2458 1122 2660 1442 8941 5692 cm pod 6699 9184 0 2296 3381 1207 2220 1949 2347 1223 2943 1579 10689 6383 pod shell 10DAF 7387 9655 2712 0 2546 1492 2468 2499 2505 1371 3151 1762 10781 6490 pod shell 14DAF 11713 13899 8894 7455 0 2433 4560 4588 4084 1671 4900 2343 13620 8160 seed 10DAF 20788 23579 19860 19927 14791 0 9143 8659 9416 3486 10241 5069 20504 14118 seed 14DAF 15143 17796 13220 12963 9661 787 0 2208 3196 1164 4751 2245 16051 9689 seed 21DAF 11087 13382 9205 9436 7136 958 1171 0 1650 601 2753 1357 12633 7404 seed 25DAF 17234 19801 15785 15544 10968 2767 4603 3691 0 168 2924 1074 17641 10773 seed 28DAF 24744 27945 24686 24829 19423 8305 14750 12426 13764 0 13980

    Original URL path: http://soybase.org/soyseq/heatmap/index.php (2016-04-30)
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