Student 1 50
Local alignment identifies the conserved regions in the sequences. So if I want to calculate the percentage of nucleatides conserved between two bacterial strains of the same species, I need to perform BLAST (which is the Basic Local Alignment Search Tool) and then compare the numbers. Finally, I can have a percentange with the results I obtained.
Student 2 30
Considering that this two bacterial strains are have the same length (because they are same species) we can calculate the Hamming distance between them and turning this distance to a percentage of difference. Then %100 - %difference = % of nucleotides conserved
Student 3 50
I can find nucleotide numbers of the two strains of two species’s with taxonomy browser in NCBI. And I can reach all of the accession numbers of one bacteria strain with using txid in nucleotide databases. If I paste all the accession numbers of one species’s strain into BLAST and if I compare with the other strain of species, BLAST will give me an average nucleotide identity percentage.
Student 4 40
Average nucleotide identity (ANI) is a category of computational analysis that can be used to define species boundaries of Archaea and Bacteria. Average Nucleotide Identity (ANI) is a measure of nucleotide-level genomic similarity between the coding regions of two genomes. We can do it with blastn. We can do the search then filter it with Percent Identity.
Student 5 70
First of all, we need the accession numbers to compare percentage of nucleotides in two species. In NCBI, we choose the database “nucleotide”, and then entrez the first bacteria name. After we search, we choose the accession numbers in summary. We take the accession numbers that how many we need. We must copy all accession numbers. Then we open the BLAST and NUCLEOTİDE BLAST. paste the accession numbers to”Enter Query Sequence”. Then in “Choose Search Set - organism”, we search the other bacteria. Then we will saw a table, we can see the percentage of nucleotides there.
Student 6 70
I find the accession numbers of the two strains by searching the organism:expand from the ncbi nucleotide database. Then i use BLAST. I enter one of the bacterial strains accession number. Then i enter another bacterial strains accession number to subject. Then blast shows us the similarity and difference. I look the table and I find the similarity ratio by dividing the amount of similar(positives and matches) ones by the total amount of nucleotides. It gives me a percentage.
Student 7 80
I use BLAST for this. First of all I download genome sequences of two strains from NCBI genome. I click Align two or more sequences button. Then I upload the sequences that I downloaded to BLAST nucleotide database. After that I click the Blast button. I can see the average nucleotide identity in a column.For instance I choose species as Escherichia coli O157:H7 str. Sakai and Escherichia coli str. K-12 substr. MG1655 and I found 98.68% Average Nucleotide Identity.
Student 8 30
There some methods to do that. We can use Conserved Domain (conserved domain architecture retrieval tool) page of NCBİ by going further with https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi?cdsid=QM3-qcdsearch-150785FABDBFF7F8&tdata=qopts. In NCBI by searching a species in nucleotide we find the accession number of two different strain and copy paste to conserved domain search. It will give us the percentage of conserved domain or we can use blast by searching certain conserved domain such as 16srrna to find the FASTA sequence or accession number.. In BLAST we can write two different accession number of strains from same species and BLAST it. we can check the alignment part and calculate the percentage.
Or another way also percentage identity means that how many letters similar are. so we can use we can use hamming or leveistein distance to calculate the percentage of similarity for nucleotides, by using dot plot . Or we can use scoring matrix it gives better result for the similarity than dot plot. so we can calculate the mismatches, similarities and difference.
Student 9 80
To compare two genomic sequences, one should align them first and foremost. A pairwise alignment is placing the two sequences face to face, and inserting gaps where necessary. BLAST is a great tool for such a purpose. It is a local alignment search tool, which means you can compare genomes to genomes when you expect that a part of the query is similar to a part of the subject. Thus, it can also be used to compare whole genomes. I would use BLASTN (Blast Nucleotide) and upload the whole genome sequence of one strain as a query. Then, from Choose Search Set I would choose the other strain (Organism option) and blast. Once I obtain the results, I see a column called percent identity, which corresponds to the similarity between the query and the subject or the percentage of nucleotides conserved between them.
Student 10 50
Average Nucleotide Identity is used on nucleotide BLAST . For example Acidicapsa sp. (NCBI:txid1872106[Organism:noexp] ) and Acidicapsa sp. CE1 (NCBI:txid10788459) for these two strain we entire accession number and organism taxid finally compare their the percentage of nucleotides.
Student 11 30
Firstly, the genome sequences of the strains should be fragmented and the nucleotide sequences should be localized in the genome using BLAST for search engine.
Secondly, local alignment occurs to compare two bacterial strains.
Student 12 80
First of all, we should use local alignment and as a tool to measure the percentage of similarity between these 2 strains, we must use BlastN. We should take one strain’s accession numbers or fasta sequences by using the nucleotide database in NCBI. After that, we should write it in the query part of blast and for the subject, other strain must be selected. When we search it by choosing nr/nt and megablast section we will get the similarity percentage between them.
Student 13 70
I would search in NCBI nucleotide database for “(name of the bacteria[Organism]) AND name of the strain[Strain]” and then take the accession numbers list. Then I would do the same to same bacteria’s other strain and take their accession numbers list too. And then I would do BLAST to align by following steps of: “NCBI - BLAST - nucleotide to nucleotide - align two or more sequences” and enter accession lists. I can calculate the percentage by dividing the number of the same nucleotides to the total number of nucleotides and multiply by 100.
Student 14 30
I can use local alingment to identify conserved nucleotides using. I would use Nucleotide BLAST for the comparison and from the data I can find how percentage of the nucleotides are conserved.