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Bioinformaticamente

A journey into the world of bioinformatics

Tag: Phred

4 Posts

Files in bioinformatics

SAM & BAM

3 March 2021 — 0 Comments

Files in bioinformatics

FASTQ does it better!

4 February 2021 — 0 Comments

Files in bioinformatics

Fasta and Furious 2 !

20 January 2021 — 0 Comments

Bioinformatics for Genomics, Bioinformatics for Transcriptomics

Cleaning is important

5 December 2020 — 0 Comments

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Alignment and Multi-alignment (1)
Bioinfo News (3)
Bioinformatics for Genomics (6)
Bioinformatics for Transcriptomics (4)
Bioinformatics tips (1)
Files in bioinformatics (4)
Know your computer (1)
Learn about bioinformatics (7)
Other (1)
Programming (1)
Sequencing techniques (5)
Tutorial (4)

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What to ask to a sequence? Hello, how are you? I hope so. Today I am writing because I wanted to share with you some exercises that I usually try to do to practice as well as for pleasure. For example, sometimes I download a sequence on NCBI or recover this from the bioinformatics course that I followed during my master’s degree and almost for fun, I ask this what it has to tell me. No I’m not crazy, on the contrary I believe that one of the basic tasks of bioinformatics is precisely that of extracting information from the biological data at its disposal, so just as an investigator squeezes information from a questioned subject, I ask this sequence what it has to say. I think this is a useful exercise for many especially to train the tendency to ask the right question in front of a biological data. In fact, depending on the data, the question changes so to obtain correct information it is necessary to ask the right question, after all as Immanuel Kant said: “Before evaluating if an answer is correct, one must evaluate whether the question is correct.” READ MORE LINK IN BIO with VIDEO TUTORIAL!!! #bioinformaticamente #bioinformatics #bioinformaticslife #bioinformatica #computationalbiology #bio #computerscience #datascience #biology #sequence #ask #ask #database #getorf #orffinder #coding #codinglife #CDS #cosingsequence #dna #rna #protein #transcript #transcription #database #bioinfo

How to retrieve one or more biological sequences? One of the most frequent operations I do during the day is the search and recovery of biological sequences of interest. So I think it is necessary to talk to you about how this can be done, especially for novices, and therefore be able to “play” with some recovered genes or proteins. I remember that at the beginning of my bioinformatics studies I enjoyed recovering gene sequences and I was delighted to observe that multitude of letters (relating to the nitrogenous bases) that followed one another within the sequence. In short, obtaining a biological sequence of interest is a basic skill for a bioinformatician and with this article I will explain how to do it.

What is a gene? You know recently I have often sat in front of the computer intent on writing something more technical and therefore to present you more in-depth bioinformatics analyzes but I have always found myself in difficulty because I realize that sometimes to better understand a certain type of bioinformatics analysis it is also necessary to know some fundamental concepts of molecular biology. So the question I've always asked myself is: Should I first write something about basic concepts, such as what is a gene, before presenting some useful bioinformatics analysis? Well yes. I have chosen to talk to you about a topic that I think is a prerequisite for understanding what comes next and therefore some very useful bioinformatics analyzes. In particular, with this article I intend to explain what a gene is and what types of analyzes we can therefore perform when we have one of these in our "hands". READ MORE....LINK IN BIO #bioinformatics #biology #molecularbiology #molecular #dna #gene #genes #rna #mrna #rrna #trna #smallrna #promoter #cisactingelement #transelement #genome #bioinformaticslife #bio #computationalbiology #transcription #transcriptionfactors #rnapolimerase #polimerase #splicing #alternative #genestructure #orf #cds #sequence #bioinformaticamente

SAM & BAM. Hi. How are you? I hope so. I have decided to delight you with a new article that will go straight into the column "Files in bioinformatics", in which I talk about the most common and important file types used by bioinformaticians. In fact, today we talk about files SAM, or of Sequence Alignment Map file, and its cousin file BAM in full, Binary Alignment Map file. These are extremely useful files as they are produced by the process of aligning (or mapping) reads on a reference genome (also called reference), this is also called re-sequencing, although in my opinion this term is a bit misleading. In any case, the SAM and BAM files are equally useful for identifying the polymorphisms that exist between a sequenced and a reference genome as well as with a third genome also aligned on the same reference, or even a fourth, a fifth and so on. In short, these files are essential to obtain the so-called "call" of the variants existing between the genomes being compared.

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