Summary
Resource Type
Transcriptome Assembly
Name
de novo American Beech (Fagus grandifolia) - ABall_v2
organism
Program Version
8.0.2
Date Performed
Thursday, August 14, 2008 - 21:00
Data Source
Source Name
: de novo assembly
Source Version
: 081508
Program, Pipeline, Workflow or Method Name
SeqManPro
Number of contigs
8319
Average Contig Length
362
Description and Download
Description: 

This transcriptome assembly was originally hosted on the Fagaceae Genomics Web (FGW).

FGW Name ABall Unigene V2
Date 2008-08-15
Software SeqManPro
Software Version 8.0.2
Number of Contigs 8319
Libraries Included in Assembly 2 (ABWP1, ABWP2)

Assembly Statistics

Number of Transcripts 8,319
Transcript N50 371 bp
Transcript Average Length 362 bp
Number of Proteins 2,383
Protein N50 135 aa
Protein Average Length 141 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 Description Library Code Platform 454 Reads 454 Bases
American Beech, combined tissue samples 1 ABWP1 454 GS FLX 35,424 9.3M
American Beech, combined tissue samples 2 ABWP2 454 GS FLX 28,829 7.7M