BLAST

2013-10-22T15:07:56Z

120266056:

BLAST is a [[Database|primary sequence database]] searching algorithm that enables you to compare a [[DNA|DNA]] or [[Protein|protein]] sequence of interest to other known sequences, allowing you to find regions of similarity between them <ref name="BLAST webpage">http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>.  

The results of a BLAST search give a graphic summary of the amount of alignment between the query sequence and the sequence hits from the database. The database sequences which produce significant alignments are shown in a table, which tells you the protein that the sequence codes for. Each has an [[Accession number|accession number]]; clicking on this accession number allows you to see the souce organism of the protien, as well as giving links to papers on the protein. The E value ([[Expect value|Expect value]]) is the staistical significance threshold; it gives the number of hits that are likely to be found by chance, therefore a lower E value will result in better matches as the probability of a chance result is less.

Identities are identical matches and can be seen as a letter between the two strands. Positives are conserved substitutions and can be seen as a (+) between the two strands.

The Blast web page can be found at: [http://blast.ncbi.nlm.nih.gov/Blast.cgi http://blast.ncbi.nlm.nih.gov/Blast.cgi]

== Basic Blast Programs ==

There are 5 different BLAST programmes depending on the type of sequence you are studying:  <br>

{| border="3" cellspacing="1" cellpadding="1" width="468"
|+ A Table Showing a Brief Description of the Five Basic Blast Programmes
|-
| [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome Nucleotide blast (blastn)]
| Search a nucleotide database using a nucleotide query
|-
| [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome Protein blast (blastp)]
| Search protein database using a protein query
|-
| [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&BLAST_PROGRAMS=blastx&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome blastx]
| Search protein database using a translated nucleotide query
|-
| [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&BLAST_PROGRAMS=tblastn&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome tblastn]
| Search translated nucleotide database using a protein query
|-
| [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&BLAST_PROGRAMS=tblastx&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome tblastx]
| Search translated nucleotide database using a translated nucleotide query
|}

  <ref>Information for the table taken from http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>

BlastP, allows you to compare an [[Amino acid|amino acid]] query sequence against a protein database. BlastN enables you to look at a [[Nucleotide|nucleotide]] query sequence against a nucleotide sequence database. Using BlastX you can compare a nucleotide query sequence translated in all [[Reading frame|reading frames]] against a [[Protein sequence|protein sequence]] database. With tBlastN you can see the similarites between a [[Protein|protein]] query sequence and nucleotide sequences from the database, dynamically translated in all reading frames, and finally, tBlastX allows you to compare the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database <ref name="BLAST webpage">http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>.  Links to these programs can be found in the table above.

The [[Low complexity|low complexity]] sequence means a region with an abnormal structure that can cause problems when searching for a sequence similarity. They can often be inspected visually as their sequences are usually repetitive e.g. CCCCCCCGGCCCCCCGGGG. It is necessary to remove these from the search because it can give results which are not entirely true, as in it may not be due to shared homology.

== Specialised Blast Programs ==

There is also the option to perform more specialized BLAST searches such as a primer BLAST search. Links for these searches can be found below to main BLAST search links.

== References ==

<references />

G1

2012-11-30T15:16:21Z

120266056:

G1 phase (or post-mitotic phase) is one of the four phases of the [[Cell_cycle|cell cycle]] and occurs in stage one of [[interphase|interphase]]. G stands for Gap and the 1 represents first so the G1 phase is the first gap phase. During this phase, the cell increases in mass carrying out protein synthesis and other cellular functions, ecxcept [[DNA replication|DNA replication]]. This phase includes the G1 checkpoint which is an important control point in the cell cycle. During this checkpoint the cell normally becomes committed to [[DNA synthesis|DNA synthesis]]. However, it can enter a quiescent resting state, [[G0|G0]], a paused stage where they can then enter G1. The [[chromosomes|chromosomes]] each contain only one [[molecule|molecule]] of [[DNA|DNA]] and are not visible <ref>Interphase website http://biology.uoregon.edu/reference/ort_mitosis/interphase.html</ref>. <br>

It is contolled by activity of cyclin-dependent kinases.<br>

=== References: ===

<references />Bruce Alberts, 2008, Molecular biology of the cell, 5th edition, New York, Garland Science

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BLAST

G1