Fasta and Fastq are text-based formats for storing sequences. Parsing Fasta and Fastq is the routine work for bioinformatics researchers.
Kseq is a small and terse library for parsing the FASTA/FASTQ format. it can parse both FASTA and FASTQ format and even a mixture of FASTA and FASTQ records in one file.
Example command line for compiling a program using Kseq library:
gcc test.c -o test -lz
R2A Medium (R2A Agar) is a culture medium for culturing oligographic bacteria. It is usually use to count the bacteria in drinking water treatment and distribution systerms. Here is the R2A Agar recipe:
Proteose peptone 0.5g
Casamino acids 0.5 g
Yeast extract 0.5g
Dextrose 0.5g
Soluble starch, 0.5g
Dipotassium phosphate 0.3g
Magnesium sulfate 7H2O 0.05g
Sodium pyruvate 0.3g
Agar 15g
Final pH 7.2 ± 0.2 @ 25 °C
Add ddH2O to 1000ml
SOC (Super Optimal Broth) Medium is a nutrient-rich medium used for bacterial culture.
The following is SOC medium recipe for 1 L:
20g Tryptone
5g Yeast Extract
0.5g NaCl
0.186g KCl
0.952g MgCl2
Add ddH2O to 1000ml
Adjust pH to 7.0~7.5 by adding concentrated sodium hydroxide (10N NaOH), autoclave to sterilize, add 20 ml of sterile 1 M glucose immediately before use.
Similar with TAE Buffer, TBE is also a buffer commonly used in molecular biology experimets.
5X TBE Buffer Recipe:
53 g of Tris base
27.5 g of boric acid
20 ml of 0.5 M EDTA(pH 8.0)
Add ddH2O to 1 Liter
When using, dilute the stock solution by 5x in ddH2O. (For example, adding 200ml 50X TAE Buffer to 800ml ddH2O)
Although 10X TBE Buffer can also be make as the stock solution, it much more likely precipitate than TAE. So, 5x is a better choice.
TAE Buffer is usually used in agarose electrophoresis for the separation of nucleic acids such as DNA and RNA. The following is the TAE buffer recipe:
50X Stock Solution of TAE Buffer:
Tris base: 242g
Glacial Acetic Acid: 57.1ml
0.5 M EDTA: 100ml
Add ddH2O to 1 Liter and adjust pH to 8.5 using KOH.
1X Working Solution of TAE
1X working solution of TAE buffer is made by simply diluting the stock solution by 50x in ddH2O. (For example, adding 20ml 50X TAE Buffer to 980ml ddH2O.
See Also: TBE Buffer Recipe
High throughput sequencing platform, namely the second generation sequencing can produce thousands or millions of sequences in a short time with a relative low cost. Now it was widely used in metagenomic sequencing and other biological field. Currently, there are mainly 3 high throughput sequencing platform:
1. 454 pyrosequencing
GS FLX Titanium
http://www.454.com/
2. Illumina (Solexa) sequencing
Illumina HiSeq 2000
http://www.illumina.com/systems/hiseq_2000.ilmn
3. SOLiD sequencing
The SOLiD™ System
The concontrations of DNA and RNA can be calculated by measuring their optical density (OD260), and the purity of these nucleic acids can be estimated by the ratio of OD260 to OD280. The following is a Nucleic Acids Calculator, The concentrations of dsDNA, ssDNA, RNA, ssOligo can be calculated easily.
Read more…
SCI Journal Impact Factor Query
The query function is coming soon….
SCI Journal Impact Factor (IF) is a measure reflecting the average number of citations to articles published in science and social science journals. It is frequently used as a proxy for the relative importance of a journal within its field, with journals with higher impact factors deemed to be more important than those with lower ones. via Wikipedia
Sequence:
341FGC: 5′-CGCCCGCCGCGCGCGGCGGGCGGGGCGGGGGCACGGGGGGCCTACGGGAGGCAGCAG-3′
518R: 5′-ATTACCGCGGCTGCTGG-3′
Target:
Bacteria 16s gene (178bp)
This primer set is design for denaturing gradient gel electrophoresis (DGGE), which was used to analyze the bacterial community in environement samples.
Read more…
Sequence:
Arch-amoAF 5’-STAATGGTCTGGCTTAGACG-3’
Arch-amoAR 5’-GCGGCCATCCATCTGTATGT-3’
Target:
Archaeal amoA gene fragments (635 bp)
Typical PCR protocol:
94°C for 7 min;
35 cycles consisting of 94°C for 60 s, 56°C for 45 s, and 72°C for 60 s;
and 72°C for 10 min.
Reference:
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., & Oakley, B. B. (2005). Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences, 102(41).
