Home   |  Other web-portals  | BdataA  | 

How to cite this? |  Junctional primer tools |  Primer designing tools  
                                  A comparison of junction-primer designing tools
                                  Balagannavar Govindkumar, Basavaraju Kavyashree and Patel Krishna (*Correspondence: Acharya KK, kshitish@ibab.ac.in)
 
Feature RExPrimer Primer Blast QuantPrime PRIMERGENS RJPrimers BatchPrimer3 (2008) MRPrimerW2 (2019) ExPrimer Ex-Ex Primer
Status* Not working Working commercial Not Working Not working not working Working Discontinued Working
Input HUGO gene name, NCBI gene ID, NCBI gene symbol, chromosome [band] Accession, GI or sequence in FASTA format Transcript ID, or user can enter the transcript sequence in FASTA format which will be searched using BLAST and identifier will be retrieved User can design different types of primers such as primers covering CpG island, primers around TSS, primers around restriction enzyme cut-site region or normal primer.
Click here for more...
Upload or paste the sequence in fasta format. Since it is Transposable elements based PCR pimer design program, 17 different repeat databases are available for selection which includes databases of a dedicated species and database of different eukaryotic species paste sequence and upload fasta file NCBI Gene Symbol, GeneBank Accission, NCBI Gene ID, Aliases, keyword Upload gene genbank file, transcript ID, exon number for creating junction NCBI gene symbol, paste the gene Genbank file, upload the gene genbank file
Organism Human No option All Human, mouse, yeast, zebrafish, drosophila, C. Elegan, Guinea Pig, Anopheles gambiae No dedicated option. No DB data connected Human, Mouse, Rat, Zebrafish, Cow, Pig, Thale cress, Fruit fly, C. elegans No option Human, Mouse, Rat
Options Primers only Primers only Primers only Primers and probes Primers only Primers only Primers, TaqMan probes, primers avoiding SNP (only for human) Primers Primers and probes
Information given for the select genes Official symbol, gene type (protein-coding or non protein coding), full name of the gene, position: chr(nn)[band], size of gene, contig accession, mRNA accession, protein accession, orientation, gene ID None None None None None Gene Symbol,RefSeq ID, Gene ID, Aliases, Keyword None Official Gene Symbol, Gene ID, RefSeq ID , Ensembl gene ID
alternative splice varients of a gene displayed NA No NA NA NA None No None Yes, all the forms present in NCBI database (like NM_ and XM_)
Transcript information given in the initial pages mRNA accession, transcript structure None None None None None No None length, exon/intron sequence and flanking region information for every exon/intron of all the transcript, mRNA accession, transcript structure
Graphical display of all transcripts of a gene NA No NA NA NA No No None Yes, interactive and mouse over will provide additional information of the exons
Junctional primer selection Not primary utility, and not a user friendly feature Not the primary utility; and not a user friendly feature. However, junction primers can be designed using option "Primer must span an exon-exon junction" for field "Exon junction span" Not primary utility; and not a user friendly feature.
Click here for more...
Not primary utility, and not a user friendly feature Primary utility of software is to be able to design TE-based unique repeat junction primer. So there are various types of junction primers possible.
Click here for more...
yes Not allowed (its automated) Not user friendly Primary utility & user friendly
Option for specifying E-E junction(s)** Not available Not available Not available None Not applicable None No Not available Yes. User can enter the serial number of exons to create junction(s). User can create junction from non consecutive exons as well (new, hypothetical junctions can be explored)
One/Both primers as junction primers One One One NA One None one One or both One or both
Obtaining a pair where one primer is E-E junction while the other is from an intron No No No None Not applicable No No None Yes
Primer repeat library Human, Rodent, Drosophila Human, Rodent, Arabidopsis, Fruitfly, Rice, Mammals, Fungi, C Elegans, A Gambiae, Zebrafish None None Not applicable No No None None
Primer specificity In-silico PCR BLAST BLAST BLAST None No No BLAST BLAST
SNP validation 1. Validated SNPs,
2. All SNPs
Yes None None None Yes Yes (only for Human) None None
Options for users to choose Tm methods None Santa Lucia 1998(Default), Breslauer et. al. 1986Also salt correction methods: Owczarzy et. al. 2009, Santa Lucia 1998, Schildkraut and Lifson 1965 None Santa Lucia 1998(Default), Breslauer et al. 1986, and Rychlik et al. 1990 None None No Theoretical, arbitrary Santa Lucia 1998 (Default), Breslauer et. al. 1986, Salt Concentration, Marmur and Doty, Howley et. al., Arbitrary
Result Page Primer detail: Sequence, position, size, Tm, GC%, primer stabilityProduct details: Sequence, size, position, Chr(xx) Transcript info: ID, name, size, orientation, transcript structureTranscript structure: Length, orientation of each exons; link to FASTA and Genbank view, and BLAST GenomicProtein details: Detail of the protein translated from the submitted transcript, its accession ID, length, orientation, and CCDS.
Click here for more...
Transcript info: Transcript ID, name of the gene, EC no.Primer details: Sequence, length, Tm, GC%Product details: size, Tm, GC%, optimal annealing temperature Transcript info:NonePrimer details:Sequence, start position,length. Tm, GC%Product size:Product size a main HTML page containing the primer design summary of all input sequences; an HTML table page listing all designed primers and primer properties
Click here for more...
Gene name, RefSeq ID, Tm, Primers, product length, penalty score Result can be viewd in 2 different formats and can be downloaded in 3 different formats. Junction location, type and its source is also displayed.Primer details: Sequencesm start and end position, length, Tm, GC%, pair annealing and self annealing score, insertion type.Product details: Product size Primer details: Sequence, position, size, Tm, GC%, stability (score), Option: more details, Product sequence, Show other primer(s) , Product as well as submitted sequence
Click here for more...
URL click to visit click to visit click to visit click to visit click to visit click to visit click to visit NA click to visit
Experimental validation Yes No Yes paper not available Yes Yes No NA Yes
  *Other non-functional and/or commercial tools are not compared here (click here for a complete list)
  **E-E junction means Exon-exon junction
 
 

copyright © Dr. Kshitish Acharya K; all rights reserved