I am having an assembled fasta file (~3.7 GB in size). I tried using the web based MISA v2.1, but it accepts fasta upto 2Mb only. Is there any other alternate software which can be used for a large size dataset for filtering SSRs?
If it is a fasta file and assembled, it can't be in GBs. There is something wrong. Check before your proceed.
Dear Nazima, You may consider GMATA tool. Article GMATA: An Integrated Software Package for Genome-Scale SSR M...
Thanks Anuj Kumar.. I tried using GMATA and was able to filter the SSR motifs... Moving on to the next step that is primer designing
Hi
You can also use the offline version of Misa. Click on "Download Sourcecode" in this page:
https://webblast.ipk-gatersleben.de/misa/
You should run it under perl. For example:
perl ./misa.pl
Regards
SciRoKo software, it also can extract flanking regions, and has an add on for creating primers
18 February 2021 6,665 6 View
Hi Im seeking advice on what would be the best model of T2D and metabolic syndrome in rats Thank you
04 September 2020 3,661 4 View
We digested the brain tissue with Trypsin ( 1x) for 15 min (all steps were performed in cold conditions) and suspend the cells by pipetting up and down (3-4 times) to the single-cell suspension....
22 August 2020 5,611 4 View
I went through the cities journal website but unluckily couldn't find the template
28 June 2020 811 3 View
Hi everyone! I am trying to extract Brucella DNA from FFPE blocks. Can anyone suggest me any good kit or protocol? I checked many articles and kits but still could not find an appropriate kit or...
15 December 2019 9,767 2 View
Hello, Photovoltaics are solar energy, renewable and economical. Why are people not very attracted by the benefits of domestic use of this green energy ? Thank you
06 April 2019 8,782 19 View
The phenomenon of the greenhouse effect is a threat to the environment. What is the contribution of renewable energies in the fight against global warming?
04 April 2019 1,239 33 View
Methodology for implementing a thesis involves: - State of the art of the studied phenomenon - Study context - Introduction - Hypotheses - Objectives - Labor interest - Methodology apprehended -...
14 February 2019 6,502 16 View
The passage from micro to nano scale in indentation of materials is of concern to researchers. How does one proceed to arrive at relevant answers?
24 January 2019 5,584 2 View
in general, for healthy people, in the 3D motion analysis to define the anatomical coordinate system on segments, one frame in static position is taken by the camera, which will make segment...
10 October 2018 4,098 2 View
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
I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....
01 March 2021 3,607 3 View
I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...
27 February 2021 547 3 View
Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...
25 February 2021 6,969 3 View
I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...
24 February 2021 4,397 3 View
I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...
19 February 2021 7,006 5 View
Remote history of Campylobacter infection with reactive arthritis, and Spitz nevus (UMP). Arthropod exposure in Zika/ChikV endemic area prior to emergence of length dependent, sensory PN with...
18 February 2021 8,719 1 View
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
I am a research tech in a wildlife genetics group and my PI and I are trying to figure out how/where to put raw reads in a repository. We have capture-seq NGS from Rapid Genomics. The post-doc who...
17 February 2021 7,575 2 View
Hi, so basically... I am trying to mimic a clinically observed condition wherein a frame-shift mutation happens only at one allele of the patients, giving rise to a truncated variant which evades...
17 February 2021 1,130 6 View