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玉米基因组数据列表

已有 5379 次阅读 2008-3-19 08:03 |个人分类:生活点滴

MAGI玉米基因组数据列表

MAGI 4.0 Contigs and Singletons

727,781 Sequences

201.0 MB

 Premature mRNA

61,428 Sequences

22.9 MB

mRNA (UTR & Exons)

61,428 Sequences

17.3 MB

To facilitate analyses of the maize gene space, gene predictions were performed on the 163,390 MAGIv4.0 contigs by FGENESH v2.6 (Softberry, Inc.) using the monocots matrix and -GC -pmrna -pexons -scip_prom -scip_term parameters. This resulted in the prediction of structures for 61,428 MAGIv4.0 genes. These predictions were parsed to produce premature mRNAs, mRNAs, and ORFs. "MAGI Premature mRNAs" consist of genomic fragments that include predicted UTRs, exons, and introns. "MAGI Premature mRNAs +200 bp" additionally include 200 bases upstream and downstream of the predicted transcription start and end sites. "MAGI mRNAs" include only predicted UTRs and exons, while "MAGI ORFs" consist of only exonic coding regions (i.e., mRNAs minus UTRs). Schematics of the extracted structures are available here. Note that MAGIs can contain truncated genes. Extracted sequences were masked using the MAGI version of repeatmasker (Emrich et al, 2004), in combination with our Statistical Defined Repeat (SDRs) and Cereal Repeat databases.

Maize Expressed Genes (MEG) Downloads

MEG_Dec03 Contigs and Singletons

80,252 Sequences

13.6 MB

Maize EST Contig (MEC) Downloads

MEC_P98-Mar06 Contigs and Singletons

672,881 Sequences

59.9 MB

454 Transcriptome Downloads

454 Shoot Apical Meristem (SAM) B73

260,736 Sequences

9.6 MB

Publication:Emrich SJ, WB Barbazuk, L Li, PS Schnable (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Research, 17(1): 69-73. (Epub: 2006 Nov 9). [Full Text PDF]

454 Shoot Apical Meristem (SAM) Mo17

287,914 Sequences

10.9 MB

Publication:Barbazuk WB, SJ Emrich, HD Chen, PS Schnable (2007) SNP discovery via 454 transcriptome sequencing. Plant Journal, 51(5): 910-918. [Full Text PDF]

Other Maize EST Contig Downloads

3' B73 EST Contigs and Singletons  20,599 Sequences 3.4 MB

3' B73 EST Contigs 2,970 Sequences 588 KB

Approximately 32,000 3' B73 EST sequences generated by the Schnable Lab (Qiu et al., 2003) were downloaded from Genbank. Only those 30,356 ESTs with polyT prefixes of >7 bp (indicative of the presence of a polyA tail on the corresponding cDNA) were assembled using CAP3 (Huang and Madan, 1999). CAP3 parameters: overlap identity >=98%, overlap length >=60 bp, clipping range <=20 bp, and overhang <= 5%. PolyT prefixes were masked prior to clustering. This CAP3 analysis yielded 3,252 contigs and 16,202 singletons. GeneSeqer (Usuka et al., 2000) was used for MAGI/EST alignments with the option for specifying a particular orientation for genomic sequences (-f). GeneSeqer EST alignment display cutoff: at least one exon with similarity >= 95% and overall cDNA coverage >= 80%

3' Mo17 EST Contigs and Singletons 701 Sequences 96 KB

3' Mo17 EST Contigs 67 Sequences 12 KB



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