<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>The question is a bit vague, so I'll have to make a load of assumptions.</p>
<p>If your contigs are from a genome sequencing project, perhaps you have available raw reads as well?  If so, mapping these reads might help you to determine whether your contigs are from a unique region (coverage near expected level), from a repeated region (very high coverage), or from some random contamination (low coverage).  This is not absolute, of course, and you have to be careful with stuff like duplicate clones, which can artificially inflate coverage, especially if you are sloppy in the lab.  If you have multiple independent libraries, something that only exists in a few of them is likely a contamination.</p>
<p>Another thing I've looked for in our project, is contigs that appear to be circular (having reads that map partially to both ends).  The jury is still out on the usefulness of this (my one glaring example appears to be a misassembled contig).</p>
<p>AT/GC content might also be useful for identifying contamination, depending on the length of your contigs and the ratio in your organism.</p>
<p>16s and 18s sequences can classify contigs as pro- or eukaryote.</p>