Summary
Name
Quercus alba - Transcriptome Assembly WO454_v2
Resource Type
Transcriptome Assembly
Organism
Data Source
Source Name
: de novo assembly
Source Version
: 081508
Date Performed
Thursday, August 14, 2008 - 21:00
Number of transcripts
22102
Average Transcript Length
431
Program, Pipeline, Workflow or Method Name
SeqManPro
Program Version
8. 0.2
Description and Download
Description: 

This transcriptome assembly was originally hosted on the Fagaceae Genomics Web (FGW), which has now been archived. Sequence information is maintained here in downloadable format only.

FGW Name WO454 Unigene V2
Date 2008-08-15
Software SeqManPro
Software Version 8.0.2
Number of Contigs 22102
Libraries Included in Assembly 2 (WOA, WOB)


Assembly Statistics

Number of Transcripts 22,102
Transcript N50 448 bp
Transcript Average Length 431 bp
Number of Proteins 9,374
Protein N50 159 aa
Protein Average Length 163 aa

Download assembled data:

Contigs (fasta format)

Predicted ORFs (fasta format)

Ace file

Annotation

BLAST against the Swiss-prot protein database:

Blastx, 1e-4 cutoff - 54% of transcripts matched a swiss-prot entry

Blastp, 1e-4 cutoff - 75% of proteins matched a swiss-prot entry

BLAST against the Trembl protein database, only plant entries:

Blastx, 1e-4 cutoff - 76% of transcripts matched a Trembl plant entry

Blastp, 1e-4 cutoff - 95% of proteins matched a Trembl plant entry

SSR Pipeline

Excel file with statistics, SSR motifs and primers (84 predicted high quality markers)

Read Statistics

Raw data may be downloaded from NCBI SRA, linked below.

454 Data

Library Description Library Code Platform 454 Reads 454 Bases
White Oak above ground tissues WOA 454 GS FLX 131,630 30.7
White Oak below ground tissues WOB 454 GS FLX 119,385 21.2M
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