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MAGI玉米基因组数据列表
MAGI 4.0 Contigs and Singletons
727,781 Sequences |
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Premature mRNA |
61,428 Sequences |
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mRNA (UTR & Exons) |
61,428 Sequences |
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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 |
Maize EST Contig (MEC) Downloads
MEC_P98-Mar06 Contigs and Singletons |
672,881 Sequences |
454 Transcriptome Downloads
454 Shoot Apical Meristem (SAM) B73 |
260,736 Sequences |
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 |
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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