Overview
Analysis Namede novo American Beech (Fagus grandifolia) - ABall_v2
Transcriptome NameFagus grandifolia 081508
MethodSeqManPro (8.0.2)
Source (081508)
Date performed2008-08-15
Number of Contigs8,319
OrganismsFagus grandifolia
An assembly of 64,253 American Beech 454 sequences and 350 American Beech ESTs from Genbank by the SeqManPro assembly software.

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
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