Computational protocol: Skin transcriptome profiles associated with coat color in sheep

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Protocol publication

[…] Raw reads were cleaned by removing adaptors and low quality reads before assembly. Unigene assembly was carried out using the short reads assembly program, Trinity (http://www.genomics.cn). Blastx alignment (e-value < 0.00001) between the unigenes and protein databases (nr, Swiss-Prot, KEGG and COG) was performed, and the best aligned results were used to decide sequence direction of the unigenes. If results of different databases conflicted with each other, a priority order of nr > Swiss-Prot,>KEGG > COG was followed when deciding sequence direction of the unigenes. If a unigene was not aligned to one of the above databases, ESTScan software was used to determine its sequence direction. Unigene sequences were first aligned by blastx to protein databases and then aligned by blastn to nucleotide database nt (e-value < 0.00001), retrieving proteins with the highest sequence similarity with the given unigenes along with their protein functional annotations. Proteins with the highest ranks in the blast results were taken to determine the coding region sequences of unigenes. Coding sequences were translated into amino acid sequences with the standard codon usage. Gene Ontology (GO) functional annotation was based on nr annotation []. Blast2GO program (http://www.blast2go.com) was used to assign GO annotations, and WEGO software (http://wego.genomics.org.cn/cgi-bin/wego/index.pl) was used to perform GO functional classification for all unigenes. […]

Pipeline specifications

Software tools Trinity, BLASTX, ESTScan, BLASTN, Blast2GO, WEGO
Databases UniProt KEGG
Application Transcription analysis
Organisms Ovis aries