Animal Genomics - Science topic

is there any ways that i can find genome similarity of an organism without whole genome sequencing ,like using maths formulas or experimental progress ?

Greetings everyone.

I seek guidance from individuals experienced in NanoPore sequencing of whole genomes of non-model eukaryotic organism. Our objective is to sequence the genome of an amphibian species with a sizable genome (~5 Gb) utilizing the NanoPore long-read sequencing platform. Despite employing various DNA extraction and purification methods, achieving the requisite purity for DNA extracts has proven challenging.

After numerous attempts, we have managed to produce samples that meet the quality standards set by Oxford NanoPore, with A260/A280 ratios ranging from 1.8 to 2.0 and A260/A230 ratios from 2.0 to 2.2. The DNA is not fragmented based on a simple TBE agarose gel run. We initiated library preparation with 1 microgram of input DNA, in accordance with the genomic DNA sequencing protocol using the Ligation Sequencing Kit (V.14 chemistry).

However, our sequencing results have consistently fallen short, with a read N50 value of less than 8 kb (somethimes much less) and a maximum output of 5 Gb (after 36h sequencing, load the lib. twice), significantly below our target. I am reaching out to seek insights from experienced individuals regarding potential reasons for these suboptimal outcomes and to explore strategies for improvement. Your expertise and guidance in this matter would be greatly appreciated. Thank you.

I attach an agarose gel picture with our input DNA sample (first spot). The corresponding NanoDrop purity ratios for this sample are A260/A280 - 1.854 and A260/A230 - 2.088.

Hi everyone!

We isolated and sequenced our nuclei, and performed hashing prior to sequencing by combining four samples in a single batch, with each sample being stained with a different TotalSeq B hashtag antibody. I am curious whether the 10X Cloud Analysis tool can support the demultiplex Cellranger pipeline for our specific case.

Thank you for your help.

Let's suppose there's an ecology investigation going on. The most relevant species of insects in a mountain range should be sequenced because they want to make a phylogenetic tree using bioinformatics software. How much would cost the sequencing at a decent quality, for each insect? Is it still too expensive to try something like sequencing the genomes of the 1000 more relevant species of an area?

I am trying to design primers for RT-qPCR. I have downloaded and aligned the available gene sequences from NCBI. As I am working with a non-model organism, I have to rely on other closer relatives and the sequences available in NCBI. I have tried both with the gene and mRNA, and tried to find conserved regions using Bioedit. Both the time, conserved regions were not enough to design a primer.

Is there any other method I can use to find conserved regions or Bioedit do a good job?

Also, if I don't find conserved regions, can I just design primers from a couple of closely related species using exon-exon junction in the hope it will work out?

The project's budget is 12,000$ does not include buying any equipments except (for example) a genotyping analysis kit, I did a project for analyzing genetic diversity and selection signatures in four endangered cattle breeds using Illumina BovineHD kit but it was not satisfying, any suggestions? it is very important and crucial for my career.

Thanks in advance,

I have received the annotated data for NGS WGS and we have done some analysis like sequence similarity distribution among species, score distribution of the biological process, etc using Omicsbox. Then we thought of comparing the complete sets of protein and gene (more than 5000 in Fasta format) with protein and gene sets from few other species. Is it possible and how it can be carried out.

I am new to bioinformatics, kindly guide me

Since two decades we came across many tools to edit the desired gene and genome viz., clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), (2) transcription activator-like effector nucleases (TALENs), (3) zinc-finger nucleases (ZFNs), and (4) homing endonucleases (HENs).

Among them which is the best tool for editing the gene of interest?

One of the steps during the preprocessing of the data from metatranscriptomic analysis is to remove any host reads (host contamination) by comparing to host database. But what if there is no host reference or the closest reference is the draft genome of the same family but different genus?

Dear Researchers,

I am going to run RNA Sequencing on mouse brain samples. I have collected the samples and then I put them in the RNALATER solution and stored them at -80.

Following this step, I removed the solution and put a lysis buffer with B-mercapto according to the Qiagen kit recommendations. I followed all the recommendations on the kit.

Finally, I have analyzed the RNA integrity and I got 5.7 and 4.4

With the nanodrop, I got 30 ng/ul concentration in one sample and 28 in the other.

Does anyone have any technical advice for me, what could be the reason for the low quality of the RNA?

Attached the report for the RNA migration.

Thanks a lot.

Many of the colors used to chromosome staining are alkaline colors (for example carmine). Are colors that have acidic properties also capable of chromosome staining?

Hello researchers

I have a fresh oral tissue samples collected by Rovers Orcellex Brush , unfortunately I can not use any kit.

Please, I need trusted protocol to extract DNA from this brush .

Best regard

Dear all i am going to perform SSCP. i am using various protocols for SSCP and silver staining but i am unable to get clear results. here is a resent picture, any one who can help and guide me in this regard plz write here.

We are seeking an enthusiastic and highly motivated post-doctoral fellow to integrate into an animal genomics research laboratory (dogs, cows and poultry) in the veterinary medicine faculty in Turin, Italy. The ideal candidate will be mainly involved in experiments related to the role of oncogenic alterations and immune-interactions in canine cancers (lymphoma, melanoma and osteosarcoma). This individual will work with a group of researchers and post-doctoral fellows of veterinary animal pathology section using molecular biology, genomics and informatics techniques, in a highly collaborative, stimulating, collegial and multi-disciplinary research environment. This position will provide ample opportunities for professional development and the acquisition of cutting-edge skills in basic and comparative cancer genomics research.

We seek a talented and exceptionally motivated scientist, with a BA/BS in biology or a related field with previous laboratory experiences in molecular and cell biology. The candidate should have basic knowledge of genomics and next generation sequencing methodologies. Strong recommendations from previous research advisors or laboratory supervisors are requested.

Two-years full time contract and salary negotiable

Interested applicants please submit a CV, cover letter, and professional references. References can either be in a reference letter format or by listing the phone/email information of contact. Please submit all documents within a single file attachment to luca.aresu@unito.it and tiziana.cannizzo@unito.it

I'm trying to find any programs or published scripts that can be used to systematically identify and return a list of genes within a specified distance of a response element.

I have a list of response elements identified via PoSSuM-search, which includes genomic coordinates for each match, and need to use this list and a .GFF3 annotation file to identify all genes that fall within XXkb (e.g 100kb) of those response elements.

Evolution, Genetics, Genomics

I just keep finding data on CHOK1, CHOK, DG44, DXB11. I was hoping I could get access to quite a few CHO genomes to make genomic fingerprint comparison easy.

My backup plan is to use mouse cell line data.

Can anyone help me with the list of cattle breeds whose genome has been sequenced till date.I have a list of breeds involved in 1000 bull genomes project and Canadian Cattle Genome Project. 

Thank you

Dear all,

I'm currently working on mammal genomes. I had received Illumina NGS data and decided to use QDD (on Windows) to fish out microsatellites for PCR primer design. I've encountered some problems and hopefully someone can help me up here.

1. By following the instructions in http://net.imbe.fr/~emeglecz/qdd_installation.html, I've downloaded Active Perl, BLAST+, ClustalW and Primer3. For Primer3, should I downloaded version 2.3.7 (the C code), version 4.0.0 (Web Interfaces - Primer3 Web) or 2.3.6 (Web Interfaces - Primer3Plus)?

2. Can I use the raw data from NGS (paired ends reads, 1GB) as the input file for Pipe1 in QDD?

3. I've tried the above and my laptop is still working on Pipe2 after 12 hours. How long will Pipe2 and Pipe 3 take for a sample size 1GB?

4. Anyone has a detail workflow for using QDD on Windows to design PCR primers?

Thank you in advance for helping.

Great Day

i want to analyse region on dna of gene of known transcrition start site ,what should be region i will take upstream and downstream of tss for to get transcription binding site.

we have extracted animal genomic DNA from blood and run in gel electrophoresis showed good bands, while after digesting these genome with 4 restriction enzymes showed nothing. no bands were produced everything went away.

we used

0.5ul enzyme

0.3ul bsa solution

2ul 10x enzyme buffer 

5ul genomic dna

then incubated for 2 h and then run in 2% agarose gel electrophoresis directly. but there were no bands showed 

I amplified my PCR fragment from mouse genome, and it gave 1 band. However, when I sent it for sequencing, it gave double signal in some regions. So I would like to ask if anyone have experience how to sequencing this PCR mixture with same size. Thank you so much.

Hello everybody. I work in RDA(South Korea). I have one question. What's the powerful genotype imputation programs in animal breeding? If i consider about imputation speed, Acc et al...

nowdays, what's be used the most imputation program?(ex: Impute, PLINK, BEAGLE, MaCH, AlphaImpute, FImpute, findhap, fastPHASE, PHASEBOOK)

Good day all. Can anyone tell me what the best software is for the estimation of Ne from 50K SNP beadchip data? Can the software available handle this amount of markers, or is it going to be very time- and computationally intensive? Thank you in advance for your help. 

We have got an extensive list of IsoMir (cow genome used as map-file) after analyzing miRNA-seq data by miRAnalyzer (data were custom analyzed by s sequencing agency). Now we have the list in the following format:

SN microRNA Sample total UR total RC mature UR RC RC exact top Expr. exact /all mature* UR RC RC exact novel mature* exact/ total mature/ mature* align

1 bta-mir-191 MuBr 406 13499 bta-miR-191 400 13493 2202 FALSE 16.32 bta-mir-191-3p 4 4 1 TRUE 25 2202 details

2 bta-mir-1434 MuBr 605 12846 bta-miR-1434-5p 366 2900 1 FALSE 0.03 --- 0 0 0 FALSE 0 0 details

3 bta-mir-142 MuBr 490 8492 bta-miR-142-3p 348 6593 33 FALSE 0.5 bta-miR-142-5p 122 1872 21 FALSE 1.1 1.6 details

Please ignore the sample column. It is our code.

While clicking on the link "detail" on the last column,  we are getting as below:

Please suggest howto proceed with this?

I have BAM files from several sheep with a linkage region of interest. There are 12 putative transcripts in this region which I will need to search for possible pathogenic variants. Is there a better way than manually searching through the sequence in IGV? Thanks!

Our normal flora specially intestinal type are living in our body millions of years and this leads us to think and even believe that our genome is shared in part with our normal flora so it is impossible to survive without these organisms living in our body.I  think we should treat them as an organ of our body like liver ,spleen,heart etc...

Does anyone have any references or literature about the most important mirRNAs which play role in mice with breast cancer? mirRNAs such as mir21,155,15,16,19, 206, 335 and others are involved in breast cancer promotion/ suppresstion. I would like to know which ones have the most important role and function in "mice" with breast cancer. Can anyone help me in this area?

Hi guys!

I'm sequencing and assembling a de novo invertebrate genome of about 0,8Gb. I want to make a lane run of Illumina nextera mate-pairs, but I'm having some difficulty on selecting the size of the mate-pairs.

I saw that for de novo genomes is better if you have mate-pair-known sizes. So I was planning on doing 5kb and 10kb gel-size selection. However, the standard Illumina procedure is to make a random library of inserts ranging from 2kb to 15kb.

I was wondering how much bias it would insert for the de novo algoritm, lets say, allPaths, to assemble it? Does anyone of you have experience with that?

I don't know if I insist on trying to have the mate-pair with known insert size or if I just go for the random mate-pair library preparation (I have plenty of pair-ends already).

Any experinces you have, or papers to share, would help a lot! Thank you so much!

I am looking for mouse reference DNA from C57/129 WT mice which has been sequenced previously.

The links below indicate "clear" connections between immunology and mobile genomics, especially when we look at the case of Paleo-immunology cerca and V(D)J recombination. 

I want to compare genomes of two different species,but from the same genus. My motive is to find some different genes. what protocol or software can i use?

Usual protocols shear the DNA too much. I know a protocol using digest after putting the nuclei into low melt agarose and then using pulse field gel electrophoresis. But this one seems complex/elaborate. Is there another, more simple way? The DNA would be from insects.