Overview
Analysis Namede novo White Oak (Quercus alba) - WO454_v2
Transcriptome NameQuercus alba 081508
MethodSeqManPro (8. 0.2)
Source (081508)
Date performed2008-08-15
Number of Contigs22,102
OrganismsQuercus alba
An assembly of 203,206 White Oak 454 sequences by the SeqManPro assembly software.

This transcriptome assembly was originally hosted on the Fagaceae Genomics Web (FGW), which has now been archived.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