<p>Hi,</p>

<p>I&#39;m just an student so I&#39;m very new in the bioinformatics terms. I&#39;ve read the terms mapping and annotation in articles and webpages but i&#39;m not sure about the difference between them and I cannot find any nice info in google. At this moment I understand:</p>

<p>Mapping; Alignment against the whole organism genome. The output is the position of the sequence in the genome.</p>

<p>Annotation: Alignment against a specific protein/nucleotide/etc database. The output is the protein name, or molecule.<br />
<br />
Is this correct?</p>

<p>In that case. It is not the same? I mean, if we get the protein or the molecule we know the position in the genome isn&#39;t?<br />
<br />
My doubt is because I read in some miRNA pipeline that they do mapping and annotation in different process.<br />
<br />
Regards and Thanks in Advance</p>

Mapping is usually the process of aligning short reads to a reference sequence, where the reference can be a genome or transcriptome.

On the other hand, In the Annotation, you go much deeper by incorporating biological meaning to the sequences. In wikipedia, it says "**Genome annotation** is the process of attaching biological information to [sequences][1]."

In Genome annotation, you may map your genomic reads to validate your reference sequences or your transcriptomic reads to find the exons and the regions which do not code. But, along with mapping, you can also annotate the genome by predicting the genes using gene predictors, repeat regions, predict non-coding genes, segmental duplications, Variant and SNP analysis, Identifying the pesudogenes etc. All these also come under annotation. So, note that it is different from mapping.

Whereas in the **Transcriptome annotation**, again, after **mapping** the reads, you would still be interested in knowing the gene expression analysis, isoforms, pathway analysis, gene family analysis, functional annotation (If the transcriptome is denovo, then assigning the function to the transcript). Hope this helps you.

~Prakki Rama.

 [1]: http://en.wikipedia.org/wiki/DNA_sequence