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 searches non redundant protein databases are used. The outputs are adapted to each other and put in comparison in order to determine the best results.

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.