How to download sequence of a particular coordinate from hg19, from Santacruz Browser?

More Navonil De Sarkar's questions See All

Is there a tool?

Is there a tool that can help me to identify chromosome and coordinate of mutations formatted...

08 September 2015 4,851 2 View

Why do I get a G>A mutation in my sequencing data?

If you see most of your relevant mutations G>A, what would you infer (generally) other than any sequencing error. Chances of sequencing errors are already addressed. Data generated on Prostate...

07 August 2015 7,176 6 View

Can anyone provide a *.bed file human exome?

To be used in Genome MuSIC.

03 April 2014 222 1 View

Can you suggest a P-value cutoff for a somatic variant call?

I am using fisher exact test to call for somatic mutation. Now, if I go for any multiple correction, it appears to me as overdone. It is removing almost everything. With, 0.01 cut off on and...

03 April 2014 4,932 3 View

Is there any restriction enzyme which can specifically cut a DNA strand sensing either a stretch of 8Cs or 8Gs?

03 April 2014 2,208 0 View

What should be the minimum depth of coverage for variant call?

For calling somatic several events could happen. One is LOH. For LOH what should be the minimum depth of coverage in the paired diseased tissue which is homozygous at this locus (blood is a...

02 March 2014 1,762 3 View

What should be the minimum read depth of a minor allele for a reliable variant call?

What should be the minimum read depth of a minor allele for a reliable variant call? I would be needing some journal reference in that respect. I would like to cite it as a support for the choice...

02 March 2014 3,384 8 View

EdgeR pipeline for a differential expression?

For a differential expression with CPM, what should be the fold change cutoff for considering the expression deregulated?

01 February 2014 9,151 11 View

VCF compare: Can anyone suggest an appropriate tool?

Job is to find somatic mutation from paired (GATK) VCFs from tumor and normals.

31 December 2013 2,505 2 View

Comparing VCFs for somatic mutations?

I need to compare VCFs for somatic mutations (paired samples), including snp, indel and LOH. Is there any tool other than Mutect that I can use?

31 December 2013 819 2 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Which is suitable for use with Python? MySQL or SQL Server?

Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?

01 March 2021 3,422 3 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases...

22 February 2021 4,374 3 View

How we can measure Kemp % in wool without using of benzene?

Would you please let me to know about the methods for measurement of medullation and Kemp % on animal? My problem is that the wool sampling and sending to laboratory is not possible. So I would...

21 February 2021 7,260 4 View

How can I retrieve FASTA sequence from gene ID or UID of a Gene ? I have GeneBank IDs ?

I treid to use Entrez Batch, but it redirects me to NCBI site. Is there any script of Linux or Python through which I can download Fasta sequence of list of gene ID ?

21 February 2021 7,783 12 View

Antibody amino acid sequence database to simulation?

Hello, I need your help. I am looking for a database of antibody amino acid sequences for later simulation in a program in order to analyze their structure. The antibodies I need to test...

18 February 2021 371 4 View

Useful architecture for bioinformatics?

Hi Dear researchers In ensemble-based architectural design Which algorithms are more useful for classification? What is the difference between parallel and ensemble architecture? Thanks I am...

08 February 2021 2,727 5 View

Electron density difference maps(Fo-Fc): what is the meaning of negative densities (red blobs)?

Dear community, As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data. However, in many cases (e.g. attached image), when...

06 February 2021 2,847 2 View

Consensus sequence from ClustalX?

I am doing multiple sequence alignment to design primer for my gene. Can anyone tell me how to select the consensus sequence after alignment. I am using ClustalX for the alignment.

04 February 2021 8,872 2 View

Kejun Guo

Hi there, did you mean UCSC genome browser?

Apparently they have changed the UI a littler bit. There used to be a "DNA" link up on the top of the page (menu bar), but now it has been moved into "View". Move your mouse cursor onto "View", you will see the options, such as "PDF/PS", "DNA", "Ensembl" etc, which were in the menu bar before. Click on "DNA", it will give your options to download a segment of the genome of your choice. Good luck!

Navonil De Sarkar

Can not the view tab either. I am trying from Delhi, India

Got yoiu suggession. Thank you