BLAST Frequently Asked questions
ERROR: "No significant similarity found"
Below are common reasons that a BLAST search results in the "No significant similarity found" message.
Short query sequences: Short alignments may have Expect values above the default threshold, which is 10 on most pages, and, therefore, are not displayed. Try increasing the Expect threshold (under 'Algorithm parameters'). Also, see the FAQ Submitting primers or other short sequences.
Filtering: Some of the BLAST programs mask regions of low complexity by default. These regions are not allowed to initiate alignments, so if your query is largely low complexity, the filter may prevent all hits to the database. On the Basic BLAST pages, adjust the filter settings in the section 'Filters and Masking', under 'Algorithm parameters'. For a description of low complexity filters, see "What is low-complexity sequence?"
What is "low-complexity" sequence?
Regions with low-complexity sequence have an unusual composition that can create problems in sequence similarity searching. For amino acid queries this compositional bias is determined by the SEG program (Wootton and Federhen, 1996). For nucleotide queries it is determined by the DustMasker program (Morgulis, et al., 2006).
Low-complexity sequence can often be recognized by visual inspection. For example, the protein sequence PPCDPPPPPKDKKKKDDGPP has low complexity and so does the nucleotide sequence AAATAAAAAAAATAAAAAAT. Filters are used to remove low-complexity sequence because it can cause artifactual hits.
In BLAST searches performed without a filter, high scoring hits may be reported only because of the presence of a low-complexity region. Most often, it is inappropriate to consider this type of match as the result of shared homology. Rather, it is as if the low-complexity region is "sticky" and is pulling out many sequences that are not truly related.
It seems like the amplified genetic sequence could be just not very complex. I don't know about this leap in logic going from an error screen to "this is an alien hybrid". Extraordinary claims require extraordinary evidence so I think I'm going to stay skeptical of this until that official report gets released with this geneticist's name on it saying that this was not a low-complexity sequence.
It actually would have been nice if they released the sequence tested so anyone could plug it into the site.
Nucleotide BLAST: Search nucleotide databases using a nucleotide query
One thing I'm not sure about, the skull's DNA had X and Y chromosomes so wouldn't that mean both parents were human?