Genome Annotation and Analysis Pipeline

Using the error corrected genome, the origin and terminus of replication were determined using GenSkew (http://genskew.csb.univie.ac.at). tRNA and rRNA were predicted using tRNAscan-SE1.31^{54 (link)} and RNAmmer 1.2^{55 (link)}, respectively. Genome prediction and annotation were performed using Prodigal^{56 (link)} and the Swiss-Prot (from Uniprot) database, respectively. The other unknown predicted genes were annotated using the non-redundant protein database of GenBank. Subsequently, the amino acid sequences of annotated genes were aligned against the protein database to identify Gene Ontology (GO), KO ID, and Clusters of Orthologous Groups (COG)^{57 (link),58 (link)}.

Free full text: Click here

Song Y., Shin J., Jeong Y., Jin S., Lee J.K., Kim D.R., Kim S.C., Cho S, & Cho B.K. (2017). Determination of the Genome and Primary Transcriptome of Syngas Fermenting Eubacterium limosum ATCC 8486. Scientific Reports, 7, 13694.

Publication 2017

Swiss-Prot

Amino acid sequences Genes Genome Replication Rrna Trna

Corresponding Organization :

Other organizations : Korea Advanced Institute of Science and Technology, Konkuk University, Hanyang University

Top 5 similar protocols

Variable analysis

independent variables

Using the error corrected genome, the origin and terminus of replication were determined using GenSkew

dependent variables

Genome prediction and annotation
Annotation of unknown predicted genes
Identification of Gene Ontology (GO), KO ID, and Clusters of Orthologous Groups (COG)

control variables

Control variables not explicitly mentioned

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!