Sequence Alignments TSD

I heard you like citations!

"We’re sorry. It’s not us. It’s the monster. The bank isn’t like a man."

"Yes, but the bank is only made of men."

"No, you’re wrong there—quite wrong there. The bank is something else than men. It happens that every man in a bank hates what the bank does, and yet the bank does it. The bank is something more than men, I tell you. It’s the monster. Men made it, but they can’t control it."

Steinbeck - Grapes of Wrath

Test

I will ref in the text like so <xr id="fig:tsd_2gjx"/>.

<figure id="fig:tsd_2gjx">

Figure 2: Shown is Hex A with the alpha subunit in red and beta subunit in blue. Figure has been rendered in pymol based on PDB entry 2gjx

</figure>

Sequence searches

There are several alignment methods provided by various initiatives, who tackle the problem of sequence searches. Here some of them are applied for the Hex A protein and analyzed for the best results. For the searches non redundant protein databases are used. The outputs are adapted to each other and put in comparison.

PSI-Blast

Iterations	2	2	10	10
E-value	0.002	10E-10	0.002	10E-10
Runtime
No. hits

Table 1: Different performances of PSI-Blast.