<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>

As suggested by Pierre, BLAST will pretty much answer all of your questions. You can use the LinkOut Links (usually on the right, use CTRL+F to find them) on the NCBI webpage to get additional information.

You should note one potential pitfall though: in order to properly search for proteins, your contigs should come from <a href="http://en.wikipedia.org/wiki/Messenger_RNA">mRNA sequencing</a>, because eucaryotic DNA is likely to contain <a href="http://de.wikipedia.org/wiki/Intron">introns</a> in their sequence (which you can't make sense of that easily). If you're searching genomic sequences, finding the right BLAST parameters can be a bit tricky.

In most cases you will know a bit of information about your sequence that will help you applying the right searches. If you're going totally blind, doing a BLAST against NCBI's nr database is a good place to start (because most likely your sequence is not entirely new or unknown).

What you can try as well:

1. Trying to <a href="http://www.ncbi.nlm.nih.gov/projects/gorf/">find</a> an <a href="http://en.wikipedia.org/wiki/Open_reading_frame">ORF</a>; mRNAs proteins will have a possible translation from nearly the beginning to nearly the end; <a href="http://en.wikipedia.org/wiki/Polyadenylation">Polyadenylation signals</a> (in eucaryotes) might provide additional help (there are 3 STOP codons- think about how likely it is for a given DNA sequence of length N to contain none by pure chance)
2. Use <a href="http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi">NCBI's Conserved Domain Search</a> to classify the protein
3. There are many specialized databases to find information as soon as you know what type your sequence is; for instance, there is <a href="http://www.brenda-enzymes.org/">BRENDA</a> for enzymes or <a href="http://rdp.cme.msu.edu/seqmatch/seqmatch_intro.jsp3.">RDP</a> for rRNA.
4. If it is a protein and you are interested in structure, you might want to take a look at the <a href="http://pdb.rcsb.org/pdb/home/home.do">PDB</a>.

Sorry if this was too basic, but you mentioned you were new to biology ;-)