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Chapter 3 Weblems

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Weblem 3.1.:

actin: actin is encoded by 30 genes in mammals, including the humans. These genes are more than from 90% homologous. Humans have six functional genes for actin: 1 gene for actin in striated muscles, 1 gene for actin in cardiac muscles and 4 genes for cytoplazmatic actin. These genes were probably created by a mechanism known as endogenous duplication.

tRNA: Human have about 21,065 genes in total coding tRNAs, from which there are about 4,421 non-coding genes, 22 mitochondrial tRNA genes, 497 nuclear genes encoding cytoplasmic tRNA molecules and 324 tRNA-derived pseudogenes. Cytoplasmatic genes can be found on all chromosomes except the 22 and the Y chromoseome.

globins: The transcription of globin genes is controlled by a single locus region (LCR). This locus controlls the expression of epsilon, Gamma-G, Gamma-A, , delta, beta globulin genes (this order of gines is evolutionally fixed). The human (β)-globin locus is composed of this five (above mentioned) genes located on a short region of chromosome 11.

HOX genes: Human HOX genes are arranged into four clusters (therefore they are situated very close to one another): HOXA (HOXA1-13), HOXB (HOXB1-9, HOXB13), HOXC (HOXC 4-6, HOXC 8-13) and HOXD (HOXD1, HOXD3, HOXD4 HOXC 8-13). The cluster of HOXA genes is present on the human chromosome 7, HOXB genes on chromosome 17, HOXC genes on chromosome 12 and HOXD genes on chromosome 2.

MHC: in humans, the major histocompatibility complex is present on chromosome 6 and it contains 140 genes.

3.2) I searched for SMRT sequencing services. It lookes like Weill Cornell Medical College in NYC has this machine. Read length can range from 200bp to 2000bp. Here is the[http:// http://smrt.med.cornell.edu/ link] to the website.

The institute with the higest sequencing throughput power is Beijin Genomics Institute, which is currently housed in China, US, Japan and Denmark. It was very difficult to asses their sequencing power since they're both a public and private company, but currently their computational servers are capable of performing at 212 Terraflops of speed and have a anual storage capacity of 17 Petabites (17,000,000 Gb).

3.3) A PubMed article compared equiptment and gave this information:

The MiSeq from Illumina has a throughput of 1.6 GB/run, 60 Mb/h and a read length of 150 (read length from here )
The 454 GS Junior has a read length of up to 600 bases and a throughput of 70 Mb/run, 9Mb/h
The Ion Torrent PGM has a throughput of 80-100 Mb/h and a read length of 120 (read lenth from here )

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