Data processing task for bioinformatics
Instead of the big indent block you make by doing if(strlen(seqbuffer1) &gt; 0), do: if (strlen(seqbuffer1) &lt;1) continue;, so the entire rest of the loop can be outdented a level, making it more readable. 

Similarly, you can turn the if(!ambiguous) into if (ambiguous) continue; and outdent that block as well.

Depending on what version of C you're using, ambiguous could be a boolean instead of an int.

You could be a little more consistent with your NULL comparisons to the result of fgets() - the one in the while() condition is implicitly != NULL but the ones in the if() statements are explicitly == NULL. IMO you should be either explicit everywhere or implicit everywhere - either choice is fine, but mixing styles makes your code a bit more unclear.

assert(strncmp(seqbuffer1, "&gt;", 1) == 0); is the same as the more-easily-understood assert(seqbuffer1[0] == '&gt;'), right?

Also, you've got at least one potential bug: What if BUFFERSIZE is smaller than input line length and then seqlength > BUFFERSIZE?