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Position: Discussion forums > Bioscience biotechniques discussion forums > Bioinformatics forum and biostatistics forum
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primer design
Posted by: kumarsysu (IP Hidden, New member, 9)
Date: August 14, 2005 09:15PM
hi
what is the best software for primer design for degenerate primers, if we have the conserved aminoacid sequences of a gene from the related species. thanks kumar
Re: primer design
Posted by: mito lab (IP Hidden, Unregistered user, )
Date: August 19, 2005 07:45AM
I would strongly recommend to design degenerate primer by hands, without help of programs. Don't use program for complement DNA based on peptide sequence since I doubt programs will take full consideration of the codon usage in different species. You just need to pull down all cDNA sequences and make multiple alignement using clustalW and alignment tools like genedoc. Take special caution on primer's 3' end to avoid any degeneration. Hope this helps.
Re: primer design
Posted by: kumarsysu (IP Hidden, New member, 9)
Date: August 19, 2005 09:22PM
hi mito lab
thanks for your mail and valuable information. even, i had done the same thing you have suggested and now, iam also in the same opnion as you. thankyou kumar
Re: primer design
Posted by: kumarsysu (IP Hidden, New member, 9)
Date: August 19, 2005 09:28PM
hi mito lab
And while using the degenerate primers, i get a band at about 360 bp, while the expected band should be at 321 bp. The template used was cDNA library. Can we consider that as our expected fragment. Also, some degenerate primers yield multiple bands when using a cDNA library? can you give me your email ID? thanks bye kumar
Re: primer design
Posted by: rakesh (IP Hidden, Unregistered user, )
Date: November 14, 2005 07:58AM
sir,
I am a student of GEC,Farmagudi,Goa.I am doing my engineering and right now in final year of information technology.I am doing my final year project title:clustering of DNA sequences into meanigful groups for that i want yours help.sir if u have any better algorithm to cluster the DNA sequences & any information regarding over project then please send me on above e-mail,suggest two three algorithm so that we can choose the best one. yours sincerely, rakesh raul
Re: primer design
Posted by: monicawells (IP Hidden, New member, 1)
Date: August 2, 2006 04:01PM
Try BioInfoMan at [bioinfoman.com]. It has a very nice tool to design the primers. It is very easy to use and it is free too.
There are some unique tools in this software and I found it very useful: o Easy-to-use (the easiest!) tool to search and retrieve molecules from on-line databases. o Powerful and foolproof cloning wizard: it also includes the gene synthetic cloning, TA cloning, D-TOPO cloning and Gateway cloning that are not available in any other commercial products. o One-click to design sequencing and PCR primers. o Rare codon analysis of a sequence of any species. o Optimized reverse translation: Codon optimization for any species GC content optimization Restriction site optimization RNA secondary structure optimization. o Smart sequencing result analysis: Automatically trims the ambiguous sequences off the two ends of your results Automatically align reverse-complementary sequences Highlights the differences after alignment Aligns multiple sequencing results against a single target sequence and multiple input file formats are supported You can store your target sequences on-line (retrieved from GenBank or entered by yourself) and access them at any time. o Auto-annotate constructs: By paste just sequences, the tool predicts all common features and converts your sequences to fully annotated GenBank format. o Construct manipulation without losing annotation! o Complete restriction digestion analysis. o All types of protein and DNA sequence format conversion and manipulation: Users can do almost anything to manipulate the sequences, calculate the properties and so on. o And much more
Re: primer design
Posted by: luv kashyap (IP Hidden, New member, 1)
Date: November 22, 2006 11:17PM
best primer desin software is Primer 3 so i guess u can use that, and for calculating properties use oligoinspector
Re: primer design
Posted by: j_delma (IP Hidden, New member, 1)
Date: January 13, 2007 03:47AM
hi
how to design a primer for a peptide sequence for cloning
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