Fagus grandifolia - Transcriptome Assembly

Summary
Publication
Description and Download
Biosamples Browser
Summary
Name
Fagus grandifolia - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Organism
F. grandifolia (American Beech)
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Fagus grandifolia
Data Source
Source Name
: de novo assembly
Source Version
: 081508
Date Performed
Thursday, August 14, 2008 - 21:00
Number of transcripts
8319
Average Transcript Length
362
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).
FGW NameABall Unigene V2
Date2008-08-15
SoftwareSeqManPro
Software Version8.0.2
Number of Contigs8319
Libraries Included in Assembly2 (ABWP1, ABWP2)

Assembly Statistics

Number of Transcripts8,319
Transcript N50371 bp
Transcript Average Length362 bp
Number of Proteins2,383
Protein N50135 aa
Protein Average Length141 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 - 59% of transcripts matched a swiss-prot entry
Blastp, 1e-4 cutoff - 76% of proteins matched a swiss-prot entry
BLAST against the Trembl protein database, only plant entries:
Blastx, 1e-4 cutoff - 80% of transcripts matched a Trembl plant entry
Blastp, 1e-4 cutoff - 94% of proteins matched a Trembl plant entry
SSR Pipeline
Excel file with statistics, SSR motifs and primers (28 predicted high quality markers)

Read Statistics

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

454 Data

Library DescriptionLibrary CodePlatform454 Reads454 Bases
American Beech, combined tissue samples 1ABWP1454 GS FLX35,4249.3M
American Beech, combined tissue samples 2ABWP2454 GS FLX28,8297.7M
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