<p>Hi,</p>

<p>I have a couple of contigs, and I would like to answer questions of the following sort</p>

<p>a.) Are they unique?</p>

<p>b.) Which organism do they come from?</p>

<p>c.) Do they come from a protein encoding gene?</p>

<p>d.) What is that protein's function etc...</p>

<p>I am very new to Bioinformatics (even Bio for that matter) so any help would be appreciated. Even links to further readings. 
Thanks.</p>

<p>A contig is DNA sequence corresponding to a region of a genome, and it is an intermediate state in the sequencing and assembly of a genome. </p>
<blockquote>
<p>a.) Are they unique?</p>
</blockquote>
<p>This question is not clear. Unique with respect to what, to other known contigs? Consider that contigs are an intermediate product of the assembly of a genome, and not all the contigs are deposited into public databases. </p>
<p>The best thing you can do is a nucleotide blast of your sequence against the nr/nt database from NCBI. Use <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&amp;BLAST_PROGRAMS=megaBlast&amp;PAGE_TYPE=BlastSearch&amp;SHOW_DEFAULTS=on&amp;LINK_LOC=blasthome">this link</a> and select it from the 'Databases' menu. </p>
<blockquote>
<p>b.) Which organism do they come from?</p>
</blockquote>
<p>This is really a difficult question. It is very strange that you have a contig and you don't know from which species it comes from. You can do a blast against nr/nt or Refseq/genomic and see in which species you get the best score and p-value. Consider that since we only have few genomes sequenced for each specie, we don't know enough about intraspecific variability and moreover your contig could belong to a non-sequenced specie. You will only be able to make a guess. you will need to look carefully at the alignments and at the p-values.</p>
<blockquote>
<p>c.) Do they come from a protein
encoding gene?</p>
</blockquote>
<p>Contigs do not come from the sequencing of a gene. They correspond to genomic regions and are variable in size and contents. A contig could contain many genes or none. You can do a blast against RefSeq transcripts, but it won't be an optimal solution because mRNAs don't align well on genomic regions. </p>
<blockquote>
<p>d.) What is that protein's function
etc...</p>
</blockquote>
<p>the same as above.</p>