What is the meaning of the minLrap and maxLrap values?¶
These values are ratios of alignment lengths computed for each comparison using the BLAST software :
- minLrap = Lmatch/min(Lprot1, Lprot2)
- maxLrap = Lmatch/max(Lprot1, Lprot2)
where Lmatch = length of the match, Lprot1 = length of protein 1, Lprot2 = length of protein 2.
if minLrap=1 and maxLrap=1 => the 2 proteins both align on their whole length
if minLrap=1 ans maxLrap<1 => one of the proteins is longer than the other, or the alignment is partial. Different interpretations are possible:
- the longer protein is a modular protein (domain fusion/fission)
- there is an erroneous start codon for one of the 2 genes
- the smaller gene is a fragment (pseudogene).
- a frameshift (due to a sequencing error or not) causes a premature stop codon in one of the genes.
if minLrap<1 and maxLrap<1 => the sequences are poorly aligned. We can observe this kind of situation in the case of gene remnants.
What is the meaning of orderQ and orderB values?¶
The orderQ and orderB values give an information about the rank of the BLAST hit for a protein of the query genome (orderQ) or for a protein of a databank (orderB).
Best bidirectional Best Hits (BBH) will have a 1:1 relationship The following Best hits will have 1<=>n relationship
These indicators can be useful to identify fusion/fission events.
Which program is used to detect the repeats ?¶
Repeat detection is performed by the Repsek program.
More: http://wwwabi.snv.jussieu.fr/ public/RepSeek/
What is the “BioProcess” classification?¶
This functional classification is based on the CMR JCVI Role IDs.
This field is optionally filled in during the expert annotation process.
What is the “Roles” classification?¶
This functional classification corresponds to the MultiFun classification which has been developed by Monica Riley for E. coli (http://genprotec.mbl.edu/).
This field is optionally filled in during the expert annotation process.
What is HAMAP?¶
HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes) is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Lima T et al (2009) Nucleic Acids Res. 2009 Jan;37(Database issue):D471-8.
What is UniProt?¶
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible ressource of protein sequence and functional information.
The UniProt Knowledgebase consists of two sections:
- Swiss-Prot which contains high quality manually annotated and non-redundant protein sequences. This database brings together experimental results, computed features and scientific conclusions.
- TrEMBL which contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation.
More than 99% of the protein sequences provided by UniProtKB are derived from the translation of the coding sequences (CDS) which have been submitted to the public nucleic acid databases, the EMBL-Bank/GenBank/DDBJ databases. All these sequences, as well as the related data submitted by the authors, are automatically integrated into UniProtKB/TrEMBL.
What is PRIAM?¶
PRIAM is a method for automated enzyme detection in a fully sequenced genome, based on all sequences available in the ENZYME database (http://www.expasy.ch/enzyme/). PRIAM relies on sets of position-specific score matrices (PSSMs) automatically tailored for each ENZYME entry. The whole Swiss-Prot database has been used to parametrise and to assess the method.
What are MetaCyc Pathways?¶
MetaCyc pathways are metabolic networks as defined in the MetaCyc Database.
The presence or absence of a MetaCyc metabolic pathway is predicted by the Pathway-tools algorithm in this organism.
What is COGnitor?¶
COGnitor compares a sequence to the COG database by using BLASTP. Clusters of Orthologous Groups of proteins (COGs) were established by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.
What is FigFam?¶
“FIGfams, a new collection of over 100 000 protein families that are the product of manual curation and close strain comparison. Using the Subsystem approach the manual curation is carried out, ensuring a previously unattained degree of throughput and consistency. FIGfams are based on over 950 000 manually annotated proteins and across many hundred Bacteria and Archaea. Associated with each FIGfam is a two-tiered, rapid, accurate decision procedure to determine family membership for new proteins. FIGfams are freely available under an open source license.” (quote from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777423/ )
What is PsortB?¶
PsortB is an open-source tool for protein sub-cellular localization prediction in bacteria.
Reference: Gardy JL et al (2005) PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics. Mar1;21(5):617-23. Epub 2004 Oct 22.
What is InterPro?¶
InterPro is an integrated database of predictive protein “signatures” used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures.
What is SignalP ?¶
SignalP (version 4.1) predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks and hidden Markov models.
What is TMHMM?¶
TMHMM (version 2.0c) is a program for the prediction of transmembrane helices based on a hidden Markov model. The program reads a fasta-formatted protein sequence and predicts locations of transmembrane, intracellular and extracellular regions.
What is antiSMASH?¶
antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.
What is Artemis?¶
Artemis is a free genome viewer and annotation tool that allows visualisation of sequence features and the results of sequence analyses. It also supports all six-frame translations. It has been developed at the Sanger Institute.
Artemis is based on the Java Web Start technology. See how to use Java Web Start.
What is Circular Genome View?¶
CGView is a Java package which allows to produce high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a mean of generating visual output suitable for the web. Starting with information of one genome and the features to visualize, CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format) and completes it with labels, a title, legends, and footnotes.
CGView is based on the Java Web Start technology. See how to use Java Web Start.
You can use the CGView toolbar to navigate into the circular map.
From left to right, the buttons are:
- Zoom out
- Zoom in
- View entire map
- Move counterclockwise
- Move clockwise
- Show position in the status bar
- Show help in the status bar
- Export to file
The Legend checkbox allows to show/hide the legend. The Full view labels checkbox allows to show/hide the labels when showing the entire map.
If you click on a gene name/label the corresponding Gene window will be opened giving you access the full annotation of the gene.
What is MeV ?¶
MeV (Multiple Experiment Viewer) is a Java tool for genomic data analysis. MeV supports many different input formats, and provides an intuitive graphical interface for clustering, classification, statistical analysis and theme discovery.
MEV is based on the Java Web Start technology. See how to use Java Web Start.
What is JalView ?¶
Jalview is a free, open source program developed for the interactive editing, analysis and visualization of multiple sequence alignments. It can also work with sequence annotation, secondary structure information, phylogenetic trees and 3D molecular structures.
JalView is based on the Java Web Start technology. See how to use Java Web Start.
What is IGV ?¶
The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. It supports flexible integration of all the common types of genomic data and metadata, investigator-generated or publicly available, loaded from local or cloud sources.
It is mainly used in RNASeq and variant analysis (see for instance RNA-Seq homepage, Read Count and DESeq Analysis) to allow the visualization of the coverage of the reference genome by the reads and to qualitatively compare coverage for various samples (experimental conditions or clones).
IGV is based on the Java Web Start technology. See how to use Java Web Start.
After clicking the “Launch IGV” button the first window appears with a lower part already displaying the annotations of the reference genome (see below).
Section #1 contains genome annotations. Colors corresponding to a specific genomic object are:
- red : CDS
- yellow : fCDS
- green : tRNA
- blue : rRNA, miscRNA
To see genome coverage, users can load data in the drop down menu “File/Load from Server”. A list of available datasets for import will then appear in a new window. Tick the checkbox corresponding to the experiments to load in the browser and click “OK”.
Warning: The loading process may take a while, so please be patient!
Then, the coverage is visible :
Users can also organize the display : Example : to compare the same type of experiment user can group forward and reverse experiment. (just click and drag)
Users can enlarge the view by drag’n dropping the mouse on the area of interest.
It is possible to zoom in to see gene sequence and translation.