Mutation Analysis - Science topic

No mutation can change an animal into a human and no gene is completely known to manifest into a trait.

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Hi Does anyone know how to format an input file for MEGA X mutation analysis?

Regarding interpretation of sequence variants using ACMG rules.

Are ACMG rules PS3 and PP3 exclusionary?

In other words, if both PS3 and PP3 rules are fulfilled, can PP3 can be applied?

PS3 - Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

PP3 - Multiple lines of computational evidence support a deleterious effect on the gene or gene product -conservation, evolutionary, splicing impact, etc.

P.S - For me, they are not exclusionary.

I'm interested in studying specific missense mutations in a human gene. My goal is to determine whether the mutated region of the protein is conserved across various species. Could you please guide me on how I can use in silico tools to find homologous protein sequences and identify their conserved regions?

Thank you very much

Hello All... I am trying to install Gromacs on windows using conda i have attempted to run "conda install -c bioconda gromacs_py" but it's not working. Any recommendations shall be highly appreciated.

Dear all,

I have a problem and I do not know why it is happening. When I do my KRAS mutation analysis most of the samples come out as in the image without the predominant red line. However, some samples, as seen in the other image, show that high thymine contamination.

What I don’t understand is, why that high contamination of thymine only shows up on the KRAS codons. The rest of the sequence is clean and does not shows thymine spikes like that.

Thank you for your help.

Kind regards

I am interested in evaluating the role of silent/synonymous mutation using the CRISPR-Cas9. However, I am unable to find any literature related to it. Can you please provide data related to it?

How to calculate the ratio of the number of mismatches between reference and reads to the number of all mapped bases at each reference position when I got bam file? Comments on any program or script or any suggestions is welcome.

I am trying to generate all possible Associative Fault Mutants for a predicate.

For example: A predicate p= (a*b)*(c*d)

where * represents a logical operator viz., || or &&.

The possible mutants are

m1= a*(b*c)*d

m2= ((a*b)*c)d

m3= a*(b*(c*d))

and so on...

But, when the conditions contains 'Not' operator then what will the possible mutants?

for this predicate p= !(!(!a*b)*c)d, how to generate the possible associative fault mutants?

Any lead will be very helpful.

Hi,

i want to know if i can detect a mutation on a DNA sequence ( Sanger sequencing ) by using BioPython.

I want to know if there is a program to write to detect the position and the type of mutation in the generated sequence compared to a wild type sequence.

Best regards.

Mutational Analysis.  Will any software help? Could someone help me sort this out?

To perform HRM analysis for genotyping on CFX96 machine for the first time, BioRad recommends to use HRM calibration kit along with Precision melt analysis software. I am just wondering whether simply using any good quality DNA binding dye along with standard PCR reagents will work or not?

Overall, the Spanish Flu is likely to be deadliest epidemic in the history of world. Estimates are that 1-3% of the world’s population died from the Spanish Flu. So many younger people died in the US in 1918 that the average US life expectancy was reduced by 10 years.

It is not clear why the second wave of the virus was so much more lethal than the first. There is some speculation that there may have been a mild and deadly version of the virus, but this has not been definitively confirmed. In the ‘developed’ world, the mortality rate was generally believed to be about 2%. In other counties, the mortality rate has been estimated to have caused up 14% of a population (Fiji islands) to die.

Eventually, toward the end of 1918 the number of deaths caused by the virus began to decrease. This is believed to be because there were so many people that had already been infected and/or the virus may have mutated again to be less invasive to the lungs. It eventually ‘devolved’ to be part of the seasonal flu. There was never a vaccine developed for the Spanish Flu.

The mutations in question are variants of the SARS-CoV-2 reference genome (MN908947.3 NCBI reference) – the first isolate from Wuhan (Wuhan-Hu-1).

Different chemical mutagens are available with different modes of action.

I've bunch of exon variants which lead to non-synonymous mutation. I need some good papers where structural difference due to mutation being analyzed.

Novel Coronavirus thought to have transferred to Human from the seafood market in Wuhan, China become a one of the most dangerous viruses in the subfamily Orthocoronavirinae. According to the literature, the genome size of RNA of this viruses are greater than 20 kilobases.

Genetic engineers has committed to change the genes of some organisms to create new features of them, and this can be applied for the Coronavirus as well.

I would like to discuss this matter with Genetic Engineers, Biologist and Scientists.

would like to understand the genomic features and structural prediction techniques of rotavirus

I have found variants in a gene in which I have done in-silico analysis for and it is thought to be disease causing. If I want to study these variants more and see their effect, would it be justified to mimic them on animal model?

there seems to be lack of studies on specific variants or mutations in that gene, but there have been a lot of studies on knockout mouse models that makes it kind of known for us what would happen if the protein has a disfunction or not functioning at all.

So I am thinking, animal model and study the variants? Or to use cells and check if the gene will be dysfunctional and report it that way only ( and then explain what we think the outcome will be based on the status of our subjects who have the mutations and the published papers of the knockout mice)??

Hi, I'm working on a variant analysis to detect disease-causing variants in Mucopolysaccharidosis IVA patients. I'm using Sanger sequencing method which includes exonic regions and a minimum of 100 bp intronic sequences from both ends of exons. However, I couldn't find pathogenic variants in several patients. Is it possible if that patients do not have pathogenic variants in exon/splice site despite showing disease characteristics? Thank you

Preferably, some database that does not take long to respond and whose input is not so complicated. Thanks in advance!

I'm working on NrCAM gene mutation. I'm searching to know about any known mutations recorded in NrCAM gene. But I'm not getting any databases or articles regarding that. Can anyone suggest me any mutation database or links to know about the mutations of NrCAM gene in humans.

In my experiment I have checked the bacterial mutation frequency after different treatment. The treated bacteria were spread in a plate containing an antimicrobial. The mutation frequency was calculated as the ratio of grown colony no. and the no. of seeded viable colony (as observed in plate without supplementation). But in case of no growth observed in plate, how to write the result. I have confusion in > or < sign. A result is enclosed for your clarification.

I've sequenced 4 genes from gene cluster - alcohol dehydrogenase family genes. My problem is with one gene in the middle - the most important for me unfortunately. I use MutationTaster, Condel and PON-P2 softwares for protein function prediction and only with this one I always get problem with transcripts and no results. I have 2 known SNPs within these variants and I checked databases - everything is correct. Where can be the problem?

Kind regards, Paulina

CRISPR Cas9 compare to other genomic editing tools

hello every one.

I am working on CRISPR/Cas9 and developed transgenic plants for mutation analysis. During tissue culture i can,t get the plants and the callus not going to green and its goes to yellow or black and last its die and cannot regenerate into plants. please give me a valuable suggestion about this. Thanks

I am currently performing mutation analysis of a gene by Sanger sequencing. I wanted to look for level of deleterious effect of that mutation on the protein.

Hi,

We are trying to do the emulsion PCR for screening of mutant alleles by following the procedure mentioned by Diehl et al (Nat Med. 2008 Sep; 14(9): 985–990) and Dressman et al ( PNAS July 22, 2003 vol. 100 no. 15 8817–8822). We are using Tegosoft DEC, ABIL WE 09 and mineral oil in the ratio of 73%, 7% and 20% respectively as mentioned in the protocol. 600 microL oil was first prepared by following the above ratio and it was layred over 150 microL aquous phase. A 5mm steel bead was added and the mixture was fractionated at 15Hz x 10s and 17Hz x 7s. The emulsion was divided into PCR tubes and PCR reaction was started. Up to this point it was OK but unfortunately the emulsion was breaking after 10-15 cycles. The oil and water phase is getting separated. We are getting cross reaction, may be due to this. We even tried different ratios of the above reagents as mentioned in the original patent. Nothing worked.

I have written to different persons regarding this but didn't get any reply. 

If anybody can help in this matter it will be of great help.

Thanks.

Planning to start some transcriptome and mutation analysis and I just need some recommendations on what the best NGS machine/technique for my needs would be.

Our research group works with viral detection in human samples through PCR-based methods. We use to sequence the PCR amplicons to confirm the specific amplification of viral sequences in a Sanger-based platform (Applied Biosystems 3500 genetic analyzer). When analyzing the electropherograms generated it is common to observe degenerated bases (usually Ys and Ws) that seems to be not generated by errors in sequencing process, but to rather represent intra-host variability in the viral sequences.

This raised our interest in further investigate these candidate variations and search for possible active mutational processes, specifically we are interested in quantify the possible influence of APOBEC cytidine deaminases in generating these variations (by searching for mutations in APOBEC specific recognition sites, namely 5'-TC-3' over random candidate mutations). Is there any software, package or pipeline adapted for this analysis?

I've read about and downloaded the Minnor Variant Finder software (MVF, from Applied Bisystems), but it seems to be not suited for this question, once it was developed to identify low-frequency human variants and requires the parallel sequencing of a control sequence, which I don't know what could be in my case.

Thank you!

I know it is possible to identify germline mutations from the blood sample. But, I have serious doubt regarding detecting somatic mutations from the blood sample. 

Generally, somatic mutations are accurately identified using samples from disease-affected tissue region and from a normal region.

Here, I want to know is it possible to detect somatic mutations from the blood sample? If yes, how exactly it is carried out?

Sanger sequencing was used and now next generation sequencing is used for mutation analysis. Can you please guide me about the steps of methodology of next generation sequencing for thalassemia.

Size of genomic DNA is too large with many exons to amplify, so can it be done using a cDNA?

Hello, I just wanted to know if anyone has ever experienced anything like this, where transforming DH5-alpha cells with DNA results in the DNA itself being modified?

I have checked the sequence of my transforming DNA (plasmid is pMSCV, AMPr) and confirmed the presence of my mutations (no signs of a mixed DNA population, the electropherogram is clean).

However after using this DNA (first time by moving the DNA into a clean, new Eppendorf tube, second time by adding competent cells directly to the original tube with the DNA) to transform DH5-alpha cells, I continually somehow get the wild-type version of my gene of interest from kit minipreps. There is no sign of a mixed DNA population, the minipreps yield wild-type DNA with no mutations present.

The competent DH5-alpha cells alone do not contain ampicillin resistance and no colonies formed on my negative control plate. I'm 100% certain I'm using the correct DNA. Not sure how this is possible, but I suspect it's happened previously before with this specific mutation in this specific plasmid (pMSCV), by someone else. There is no -80 degree bacterial glycerol of this mutant (the only one made previously turned out to be wild-type too).  

If anyone has suggestions on what might be happening here, I'd appreciate hearing them.

Hello everybody,

I have a question to chromatograms.

Is it possible to determine whether a tumor mutation is heterozygous or homozygous when DNA from tumor cells is isolated and amplified by using PCR and sequenced?

I've read that if the mutation is heterozygous a single peak position within a trace may have but two peaks of different colors instead of just one and that this was common when sequencing a PCR product derived from diploid genomic DNA, where polymorphic positions will show both nucleotides simultaneously. (The University of Michigan DNA Sequencing Core Interpretation of Sequencing Chromatograms https://seqcore.brcf.med.umich.edu/sites/default/files/html/interpret.html)

The DNA which is analysed origins from several tumor cells so the chromatogram presents an average of the tumor cells, doesn't it? So how can the chromatogram make a statement about whether the DNA mutation of a single tumor cell is heterozygous or homozygous? It sounds more logical for me that it states that when I have a double peak I can just say that I have DNA strands in the tumor cells that differ from one other and the tumor is heterogenous but how can it be indicative of tumor cells being heterozygous or homozygous? Couldn't it be possible that on the one hand the tumor has cells that have the mutation and on the other hand there are also tumor cells that don't have the mutation?

I'm looking forward for answers and thank you very much.

When constructed a mutant library how to choose the number of individual transformants that need to be sequence-verified (48,96 or 192) after the random mutagenesis ?

I would like to know if it can be justified (statistically speaking) to sequence only 48 clones of the library?

I am working on one gene having 19 exons with 4 transcripts. A deletion mutation (one bace pair deletion) is present in all the four transcripts of this gene. It leads to frameshift and make a stop codon after 6 amino acids. My question is that i have done reverse transcriptase pcr and found no splice variant. After that i did western blot and got the equal amount of protein like in control what could be the possibilities, principally there should not be any protein or if so then it should be significantly reduced?

Dear Sir/Madam, 

I am working on DNA sequence (Sanger's method)  to find the SNP's for my Project work. I suspected that one of the mutation is novel, how could I prove that as a novel mutation for publication. 

what should I do now for confirmation?

Is their any alternative technique for prove?

Shall I go through RFLP? is it enough to prove or else?

Hi everyone,

which other prediction tools (in addition to Provean) could be used to predict the Impact of indel mutations?

Thanks for your help! Andreas

Hello,

I am looking for mosaics, low level mutations, within human exomes (about 5-10%). Is Next Generation Sequencing able to detect these accurately? I understand this sequencing has a high error rate compared to Sanger but if I am seeing 5-10% mutation of the same base pair is this valid and not just an error? I sequenced entire exomes (using AGRF/Macrogen), getting on average about 100 reads per base pair. Using this data I have found lots of low level mutations and some really interesting results.

Any thoughts/suggestions are much appreciated.

I am looking for the sequences of p53 pseudo-genes in different mouse species. It is on chromosome 14 (almost certain!) while the true p53 gene is on chromosome 11. Can I specify chromosome number in blast search, so that I only search against chromosome 14? 

I am an unexperienced undergraduate working in a lab and am stuck for a long time on this mutagenesis. My PCR reaction is from the protocol from my lab 35 ul water, .5 ul phusion, 1.25 ul of both primers, 50ng of template plasmid, 1ul of dNTPS, and 10 ul of buffer. 

The reaction cycles between 30 seconds at 98C to 3:30 70C ( the plasmid is around 8 kb) for 20 cycles

After that I check to see bands on the gel and they are there usually, but I don't know if they correspond to the new sequence or the old template.

Sometimes I get colonies (I get very few colonies per plate) and I am able to miniprep them and sequence, but the mutation I want is not there when i get the sequence back. Sometimes the DNA concentration is too low to send them out to sequencing. I don't know why. Also, a few times I get a lawn on the LB amp plate which is odd as this may indicate contamination?

Honestly, please tell me what I am doing wrong or any suggestions please.

Hi,

Imagine you got a mutant library of a plasmid DNA generated by random mutagenesis and affecting the whole plasmid sequence. This mutant library is going to be used to transform bacteria and check which mutations are selected.

Can you approximately estimate the probability of having deleterious mutations in known plasmid genes. For instance, what's the probability of obtaining a mutation that disable the antibiotic resistance gene? 

many thanks

I check the mutation frequency of several tumor driver genes on COSMIC

For instance, there are two data.

Total number of unique samples: 42439

Unique samples with mutations: 797

I would like to ask whether these mutations are heterozygous or loss of heterozygosity or sum of both cases. I think it might make a great difference for tumor repressor genes.

I am looking for designing crRNA against the putative G-quadruplex forming motifs. Taking account of the criteria for a good crRNA, web-based design gives crRNA sequences that don't overlap the sequence of my interest. On the contrary, manual design compromises the quality of the crRNA with lots of off-targets in the genome. However, this is very difficult in designing any primer against the sequence having tandem guanine repeats. 

Therefore, I have planned to design two crRNAs in (+) and (-) strands respective having 84 bases in between and want to ensure the deletion of the 84 bases in between by CRISPR-Cas9 method. My design of crRNA is provided in the attachment. Please help me in in this regard.

We are planning to do mutational analysis using Droplet Digital PCR and Cast PCR, can anybody suggest the best extraction methods for low ctcs (5-2000) cells? 

Under the assumption that sites under positive selection are more tolerant to mutations, can one interpret (assume) the intolerant sites to not be under positive selection?

the genes X and Y both a phenotype when mutated individually while keeping the other one unmutated but in case of a double het KO of X & Y i see a less severe phenotype than expected. why? 

I'm getting frame shift mutation in one of my mutation. I'm using wild type as template and using forward and reverse primer. Then doing dpn1 digestion. And then transformation and send for sequencing. But every time I'm seeing that mutation happens at a particular place I'm looking for , but frame shift mutation happens also. Please suggest a way of avoiding frame shift to happen

i have to identify the number of pseudo gene present in genome, what are the methods by which i can predict and identify these pseudo sequences. Please suggest me any online or offline tool or software for this query.

There are a lot of articles talking about genetic variant and more talking about mutations. At this stage if we have a clear cut definition which could clearly differentiate the variant and mutations?

How  gene polymorphism is different from gene mutation?  all gene polymorphisms contribute to disease susceptibility?

Braf exon 15 is about 220bp. After amplification the bands were proper but faint. The problem occured only during re amplification and that too only in few samples.But the reamplification of other genes on the same samples gave proper results.

2% agarose gel was used.

I intend to edit those genes using CRISPR /Cas9 tool 

Pardon my ignorance, but there are a number of papers discussing amino acids in DHFR that seem to be "off by 1". i.e. Leu22 when it is Leu23, Cys 6 when it is Cys 7, Phe30 when it is 31. It seems that those in the DHFR field are ignoring methionine 1. Is that the case? And if so, why?

We are studying a gene with 5 exons. In a patient with a mutation in one of the introns we detect a splicing defect such that exon 3 is missing (exons 1,2,4,5). Yet we also detect the wild type variant containing exon 3 (exons 1,2,3,4,5). I can design an oligo that spans the exon 2,4 junction to measure specifically the variant that lacks exon 3. But if I want to compare the relative levels of the two variants in the same cell by qPCR, how would I do that? Oligos that anneal to all other exons will be in common between the two variants.

I have a plasmid which differs by one base from wild type. This base will change the protein by one amino acid, hence I need to mutate that base which is residing in the central part of the plasmid. Is inverse PCR the only option for it? 

Now about designing the primer for inverse PCR- 1) Where should I put the mutated base - terminal or central position of the primer?

2) Should I put the mutated base in both forward and reverse primers or either of them?

Please illustrate with an example if possible.

Thanks

Following CRISPR mutagenesis and sequencing analysis of the F1s, I have found a heterozygous male with 10bp deleted on exon1 and a heterozygous female with 5bp deleted on exon 1. I was wondering if there is specific term that would be applied to F2 offspring that would inherit both these mutations, because this is not homozygosity. Thank you.

I am trying to study the effect of mutating or deleting different TFBS (one at a time)in the promoter region of a gene of my interest(a mouse gene),by cloning promoters containing the mutated sites in a pGL3 basic vector and then transfect HEK293 cells with them,i wanted to know about:

1. how should i design the primers in order to either mutate or delete the TFBS in the promoter.

2. what measures should i take in order to avoid any interference from the endogenously expressed TFs in the cell line.

Your work refers to rare mutation R360T in gene KCNQ1 however only very briefly, can you recommend any publications or information source on this particular mutation?

would you please advise me of the best molecular technique for mutation detection in CYP21A2 

Please, I need some advice.

How to make a deletion in the middle of the gene?.

Has anybody – apart from the information provided in the original and other papers and the information available from DSMZ, Cellosaurus, Cosmic and similar sources – genetically characterized the LAZ-221 cell line in more detail in terms of fusion genes, copy number alterations, mutations, indels,… by RNA-seq, WES, or WGS and would be willing to share this information?

Thanks in advance!

The original approach from the Jaenisch lab uses two ssoligos and 2 guide RNAs.  We were lucky to have obtained one (out of 40 genotyped) mice, though a single base pair deletion outside the CRE binding site was evident; this however did not affect cleavage.  I am polling the globe to see who has had success in mice with the original method and if not, which method are you following?

Thanks all

Joe

We want to detect low abundance of mutations and differentiated expression of genes in tissue samples. We suppose that some mutations and differentiated expression of genes in the cancer cells, but not in the stromal cells. Whole sample DNA or RNA extrations may lead to artificial results, some times false negative and some times false positive. We try laser micro-dissection of the fresh samples to dissect the cancer tissue, but due to the low concentration of the DNA or RNA after extration, analysis can not be conducted. 

I am planning some experiments to determine the effect of a drug on zebrafish adults carrying a mutation of my interest. My strategy is to use a tank of F1s to obtain F2s, genotype them and then segregate them as hets, homs and wild type as I want to check whether different groups react differently. The problem though is that my first batch of F2s has yielded very few homs and wild types. So I am now raising a second batch of F2s from the same F1s. I could perform the same experiment individually on each batch or combine the two batches and do the experiment once. Statistically, I could obtain large variation between the few homs, for example, and this could be mitigated by having larger nos. of homs. However, I am also concerned about variations between different F2 batches. Any advice would be greatly helpful.

What we know about cysteine is that oxidized during the time? So, if it's the case, do you have any idea how stable cysteine mutant? I have already tried to incubate my protein sample into 1% DTT for 30 min at pH 7.5(if there is any oxidation). And I observed some differences, however, I have some doubt about the effect of DTT on my sample. Do you think the best thing to answer this question is mass spectroscopy or there is another way that ı could try and see?

hello

I am working on subcloning to insert my target protein to new vector, after the restriction, ligation,and transformation I did sequencing for the DNA by the vector primers VP1.5 nad XL39 and the result was fine the protein is inserted but there is stop codon between the protein coding sequence and the tag need to be removed. I used the site directed mutagenesis kit  to remove the stop codon then the product was transformed and sequenced again 

the XL39 primer sequence showed the stop codon was removed because it is close to the mutation site but the VP1.5 primer sequence failed (no reading at all with big blob) for all the 5 colonies that picked 

the cycling parameters as the kit protocol suggests; 25 Cycles, Initial denaturation 98 °C 30 seconds, 98 °C 10 sec, annealing 63 °C ­30 sec, 72 °C ­30 seconds/kb -the vector size is 6200 b so I extend for 4 min- Final Extension 72 °C 2 minutes

Is there any explanation for this?

I know in theory that it's possible for a non-synonymous AA substitution to have little functional effect, but can anyone provide a real-life example? I can find papers where mutations predicted to have an effect on function were then tested and found to indeed affect function, but have not found any reports of a tested substitution that was found to be functionally neutral.

we identified multiple mutations (vus) in human genes that we believe have a protecting effect against cancer.

is there any database or web tool that can be used to detect the function (and generate survival curves) of VUS in cancer patients? for example by generate survival curves of people harboring the mutation?

Dear friends

I am trying to construct few deletion mutants of Mycobacterium abscessus using the pJV53 recombineering system. I have transformed the M. abscessus cells harboring the pJV53 plasmid (carries recombinase, Km resistant) with the linear PCR product which contains the flanking regions of the gene to be deleted and the zeocin cassette. I selected the colonies in 7H10 plates containing kanamycin and zeocin. However, when I do PCR to confirm the incorporation of zeocin cassette into the gene to be deleted, I get the same band as that of wild-type. I checked the resistance of M. abscessus WT cells to kanamycin and zeocin and the cells didn’t grow in both the antibiotics.

Any help on this would be greatly appreciated.

Warm regards

Bindu

Hello all,

1. Is there anything database that helps in the identification of tumour types and relevant cell-lines where CCDN3 mutations are observed? I‘m interested in the CCND3 mutations that accrue around the phosphorylation motif at amino acid T283.

2. We have a drug that causes CCND3 degradation in cell lines. Is there any experiment to confirm our findings? Eg: looking further at expression level of genes that are activated by CCND3?

Thanks

Lax

A female patient presented with bilateral lower limb weakness for 10 years and bilateral upper limb weakness for 4 years. CAEab（+）, AchRab（+）. EMG suggests muscular impairment. No decremental EMG response of the compound muscle action potential (CMAP) was detected on low-frequency (2-3 Hz) stimulation. She had mutations in gene AGRN（c.2255-3insA） and gene MATR3（c.1778+3A>G）.No family history. Her sister and her mother had the same mutation in AGRN. Her father ha the same mutation in MATR3. Is it possible to be digenic inheritance pattern? MATR3 may interfere with splicing site of AGRN.

I want to perform site directed mutagenesis to a sequence I have cloned into a pGL4.1 vector, but I'm not sure which vector to clone the mutants in once mutagenesis is validated. I want to clone into LNCaP cells (prostate cancer cells) and perform ChIP and qPCR analysis for target genes. I am a first year graduate student and not sure how to go about deciding.

Needed for divergence and demographic expansion study.

I need to locate the mutation in the gene. I know the amino acid, the position number and the aminoacid I need to change it to. But how do I locate it in the gene?

Thanks,

Ariadna

I have a metabolic phenotype due to some unknown mutation. what are they ways to identify the location and mutation on genome except whole genome sequencing?

I need an online tool that would calculate all possible neutral mutations in a certain reading frame of a protein-coding sequence and provide me with a list of restriction sites that can be created by introducing neutral mutations. Do you know such tool? Thank you.

Hi,

I am the graduate student of bioinformatics

I got whole genome sequence through next generation sequencing and have been doing comparative analysis using it.

And I need to find the mutation rate (or change rate) from previous reported sequence because they are looked really similar but not matched perfectly. . However I can't find the way to figure that rate

I have searched for many many days through NCBI or google scholar

but I cant find anything :(

Is there a previous report or something way to solve it?

Respected all,

Our research group have conducted some study related to behavioral genetics, we are working on a microsatellite repeat in promoter region of a gene. Can we predict insilico, that variations in repeat element can effect transcription etc. If yes then what toolshould are method we can used for it? Is there any related article to this specific study ?

HOPE to see best response from researcher's 

Portulaca oleracea is a medicinal plant.is there any experience on mutation breeding of this plant using physical and or chemical mutagenesis?

Dear all,

I try to detect possible mutations within my DNA.

For this, I use the Surveyor Nuclease S Assay (Cel-I-Assay).

After heteroduplex Formation andTreatment with Surveyor Nuclease, I don´t get any product.

Strangely, I checked my DNA after PCR purification via gel electrophoresis and detected a clear and distinct band, as expected.

So, what happended to my DNA? Any suggestions?

Best regards

I am mutating 3 amino acids, or 9 nucleotides. I need to cover all combinations. If I put N on all positions, is that good or somebody has better idea, I am happy to hear it. Thanks.