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Where should I start looking for an online gene library?

Where should I start looking for an online gene library?



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Is there an online library that includes all known genes in stored in their nucleotide form of all living organisms?

I'm presuming that such a database doesn't exist. So to kick of my search, how can I find a gene amongst all the other databases? Where is a good place to start looking for information about my gene given that it is a well studied sequence? The issue is that I have been provided with the sequence, but I just don't know what organism the sequence belongs to or what it codes for.


Databases

There are too many databases to list here, but Wikipedia has a decent list of the genome databases. For example, there are databases dedicated to genes of individual species, like Wormbase, SGDB and countless others. Alternatively, as others mention a great place to kick off your search is the NCBI.

Finding your nucleotide sequence in databases

It sounds like you already have your sequence. If you want to see if your sequence has been found elsewhere or if there are any similar sequences, you can use BLAST from NCBI. Although it is not strictly a database in itself, it looks to align your sequence to similar sequences in external NCBI databases and quantifies the sequence similarity. It will reveal the species for you to go to a more appropriate database along with a lot of other information about the gene.

There are plenty of parameters to alter to suit your specific needs, but generally, the default settings are a great place to start analysing your gene. You'll need to run a nucleotide test since you want to find the DNA sequence. The results might be difficult to interpret.


NCBI is a good option. http://www.ncbi.nlm.nih.gov

If you're looking for a gene sequence, you can search for the gene name in the nucleotide database. For example, here is the annotated human insulin gene; http://www.ncbi.nlm.nih.gov/nuccore/J00265.1


SwissProt is a human-annotated database of genes/proteins with known functions.


No, you are wrong in your assumption that there is no such library.

GenBank. One-stop shop.

Blast your sequence against it on-line. If it isn't there you are not likely to find it.


GenScript Rare Codon Analysis Tool

Codon usage plays a crucial role when recombinant proteins are expressed in different organisms. This is especially the case if the codon usage frequency of the organism of origin and the target host organism differ significantly. Therefore, to enhance efficient gene expression it is of great importance to identify rare codons in any given DNA sequence and subsequently mutate these to codons which are more frequently used in the expression host. Rare Codon Analysis Tool is powerful for codon usage frequency of your sequence and codon usage distribution. It can help you decide if your sequence needs to be optimized for heterologous gene expression.

You can choose a precalculated codon frequency table from the list (E. Coli, Yeast, Insect, or Mammalian).

Please choose the origin organism.

Please only paste in sequence data, and do not include sequence title and coordinates, but could include numbers please only use letters A, C, G, and T.


Epitope Tag or Fusion Protein

Tags and fusion proteins are excellent tools for further understanding the function of your favorite gene. For example, fusing your protein to an epitope tag, such as Flag or HA, will allow you to easily identify your protein using an antibody against that epitope. This could allow you to conduct western blots or immunoprecipitations of your favorite gene even if you do not have an antibody against it. Another common scenario is fusing your protein to another protein, such as GFP, which allows you to visualize the cellular localization of your protein.

Just remember that when you are designing your plasmid you should keep your gene "in frame" with the fusion protein. This means that the final product should be translated as a single string of amino acids that preserves the sequence of your gene and of the fusion protein.

    - N-terminal Flag-HA for mammalian expression - C-terminal TEV-His6-Flag for bacterial expression - N-terminal Flag-TEV for bacterial expression - N or C-terminal 2xFLAG tag in pCS for a variety of systems, including Xenopus
    - N or C-terminal 3xHA tag for mammalian expression - N-terminal double HA tag for mammalian expression - N or C-terminal 2xHA tag in pCS for a variety of systems, including Xenopus - C-terminal 3xHA tag for yeast expression
    - N-terminal Myc tag for mammalian expression
    - C-terminal Myc-His tag for mammalian expression (Gateway) - A variety of His tagged bacterial expression vectors - N-terminal His6-TEV tag for bacterial expression - C-terminal His6 tag for bacterial expression - N-terminal His6 tag for bacterial expression (Gateway)
    - N-terminal GST for mammalian expression - N-terminal His6-GST-TEV for bacterial expression - N-terminal His6-GST for bacterial expression (Gateway) - N-terminal GST for yeast expression - C-terminal GST for C elegans expression
    - C-terminal GFP for mammalian expression
  • pcDNA3 GFP LIC cloning vector - C-terminal GFP for mammalian expression - N-terminal GFP for yeast expression - C-terminal GFP for bacterial expression - C-terminal GFP for C elegans expression
    - pEntry vector that adds a C-terminal nuclear localization signal - N-terminal FLAG and SV40 nuclear localization signal
    - pDest vector that adds a N-terminal myristoylation signal

For more information about tags, including amino acid sequences, see our list of common tags.


Next-Generation Sequencing for Beginners

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Designing Life: Should Babies Be Genetically Engineered?

NEW YORK — The increasing power and accessibility of genetic technology may one day give parents the option of modifying their unborn children, in order to spare offspring from disease or, conceivably, make them tall, well muscled, intelligent or otherwise blessed with desirable traits.

Would this change mean empowering parents to give their children the best start possible? Or would it mean designer babies who could face unforeseen genetic problems? Experts debated on Wednesday evening (Feb. 13) whether prenatal engineering should be banned in the United States.

Humans have already genetically modified animals and crops, said Sheldon Krimsky, a philosopher at Tufts University, who argued in favor of a ban on the same for human babies. "But in the hundreds of thousands of trails that failed, we simply discarded the results of the unwanted crop or animal."

Unknown consequences

Is this a model that society wants to apply to humans, making pinpoint genetic modifications, only to "discard the results when they don't work out?" Krimsky asked during an Intelligence Squared Debate held in Manhattan. He added that assuming no mistakes will occur would be sheer hubris.

He and fellow ban proponent Lord Robert Winston, a professor of science and society and a fertility expert at Imperial College in London, focused on the uncertainty associated with the genetic underpinnings of traits. The two also addressed the consequences of manipulating genes. [5 Myths About Fertility Treatments]

"Even [for] height, one of the most heritable traits known, scientists have found at least 50 genes that account for only 2 to 3 percent of the variance in the samples," Krimsky said. "If you want a tall child, marry tall."

Mother Nature doesn&rsquot care

Meanwhile, their opponents, who opposed the ban, talked of empowering parents to give their children a healthy life, even if it meant giving their offspring traits they themselves could not pass down.

Lee Silver, a professor of molecular biology and public policy at Princeton University, urged the audience members to look at someone sitting next to them.

"That person and you differ at over 1 million locations in your DNA [deoxyribonucleic acid]. Most [of these variations] don't do anything," Silver said. "[But] even if you are a healthy adult, 100 [of these] can cause deadly childhood disease in your children or grandchildren."

"Mother Nature is a metaphor," he continued. "And it is a bad metaphor, because in reality inheritance is a game of craps … It won't have to be that way in the future."

His fellow ban opponent, Nita Farahany, a professor of law and of genome sciences and policy at Duke University, attacked the idea that uncertainty should prevent the use of the technology, pointing out that reproduction, completely unaided by technology, involves much uncertainty.

"We are not going to ban natural sex," Farahany said.

Already possible

A significant portion of the debate focused on a particular technology known as mitochondrial transfer. While the majority of DNA resides in a cell's nucleus, a small amount is contained in the cell's energy factories, called mitochondria. This mitochondrial DNA is passed from mother to child. In rare cases, women have mitochondrial defects they can pass down to their children, causing devastating problems or even death.

Mitochondrial transfer can replace such defective mitochondrial DNA with that from a donor, allowing affected mothers to avoid passing these defects on to their children, who then carry genetic material from three parents (the father and two mothers, including the donor).

Opponents of a ban argued it would prevent women with mitochondrial disorders from having healthy children of their own.

"I am not here to defend every type of genetic engineering. I don't think we are ready as a society to embrace it all," Farahany said.

Rather than an outright ban, she and Silver argued for a middle ground, which would allow for certain procedures once they had been shown to be safe and effective. An emerging scientific consensus says mitochondrial transfer would fit into this category, she said.

"We know fiddling with mitochondrial DNA may make a massive difference to what happens to nuclear DNA. … Abnormal children have been born as result of mitochondrial transfer," he said. "I think, in preventing one genetic disease, you are likely to cause another genetic disease." [The 10 Most Mysterious Diseases]

Society should instead focus on the enormous importance of environmental influences in health, Winston said. "What we should be trying to do, rather than risk making abnormal babies, is to improve the environment so the DNA functions in the best possible ways."

Neither Farahany nor Silver argued in favor of allowing parents to modify their children to ensure other traits that are less medically necessary, but nevertheless desirable, such as higher intelligence or blue eyes.

"What I think parents care about most is promoting the health of their children," Silver said.

Leading to eugenics?

Both sides referred to the specter of eugenics, an idea embraced by the Nazis, which holds that selective breeding can be used to improve the human race.

Winston and Krimsky pointed out that genetically modifying children to choose desirable traits evoked this approach. Meanwhile, Farahany noted that some of the worst abuses of government in recent history involved attempts to control reproduction. How would a ban on the genetic modification of children be enforced, she asked, would all babies be forcibly tested?


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Codon Chart

The continuity of life is the result of storage, replication, and transcription of genetic code, from one generation of life forms to the other, in the form of DNA, and RNA in some cases. The subject of this article is the codon translation chart, which is an important piece of reference, to understand DNA transcription, as well as creation of the 20 amino acids.

The continuity of life is the result of storage, replication, and transcription of genetic code, from one generation of life forms to the other, in the form of DNA, and RNA in some cases. The subject of this article is the codon translation chart, which is an important piece of reference, to understand DNA transcription, as well as creation of the 20 amino acids.

Incontrovertible Evidence for the Unity of All Life

The basic building blocks of the genetic code are universal. In essence, every single unicellular and multicellular life form, that has ever existed on Earth, has had a genome, made up of the same nucleotide subunits (A, T/U, C, G). This clearly proves the common origin of all life on our planet.

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DNA (Deoxyribonucleic Acid) is the molecule that contains all the genetic code of an organism. It is the recipe book, referred by cells, to produce proteins that make body functions possible. This book is unique, in the sense that it is written using just four alphabets, which are nucleotides. It is entirely written with three-letter words, called codons. Adenine, Guanine, Cytosine, and Thymine (A, G, C, T) are the four nucleotides (or letters) that form codons (or words) in the DNA. In RNA (Ribonucleic Acid) molecule, the genetic code is made up of the four letters, Adenine, Guanine, Cytosine, and Uracil (A, G, C, U).

The four nucleotides form 64 (= 4 3 ) triplet combinations or codons. So the entire genetic code is written using just 64 different words. Each one of the codons encodes one of the 20 different amino acids. To be precise, among the 64 codons, 61 encode amino acids (including the initiation codon in RNA, which is AUG). The rest of three act as stop codons, that terminate the transcription process. More than one codon can translate into the same amino acid, which is a building block of proteins. Here is a RNA/DNA codon translator, that will directly provide you with the amino acid associated with a particular nucleotide triplet combination.

RNA/DNA Codon Translator
Enter Nucleotide Triplet Combination
Check Amino Acid

A gene is a segment of DNA, which is a series of codons that contains information about synthesis of a single or more proteins. Transcription is the process of reading a gene and extracting information from it, for protein synthesis.

The start of DNA transcription of a gene is signaled by the start codon. Stop codons signal the end of transcription. The information about synthesis of every gene is read from the DNA, in the cell nucleus and transferred in the form of messenger RNA (mRNA) segments, to the exterior cytoplasm. In there, with the help of tRNA (transport RNA molecules), the ribosomes synthesize proteins, with the right amino acid sequences.

The DNA and RNA codon charts presented below, detail the various nucleotide combinations that create the 20 known amino acids. There is redundancy in the coding, as more than one nucleotide combination maps to the creation of the same amino acid.

If you are studying or planning to study biochemistry, you will eventually study the role of mRNA (messenger RNA) in DNA transcription of the cell. The starting codon for mRNA is AUG. Here is a chart that lists the various combinations of nucleotides which lead to creation of the 20 known amino acids.

Amino Acid / Start-Stop Codon Codon (Nucleotide Triplet Combinations)
Phenylalanine (Phe) (UUU, UUC)
Leucine (Leu) (UUA, UUG, CUU, CUC, CUA, CUG)
Methionine (Met) / Start Codon (AUG)
Valine (Val) (GUU, GUC, GUA, GUG)
Serine (Ser) (UCU, UCC, UCA, UCG, AGU, AGC)
Proline (Pro) (CCU, CCC, CCA, CCG)
Threonine (Thr) (ACU, ACC, ACA, ACG)
Alanine (Ala) (GCU, GCC, GCA, GCG)
Tyrosine (Tyr) (UAU, UAC)
Histidine (His) (CAU, CAC)
Glutamine (Gln) (CAA, CAG)
Asparagine (Asn) (AAU, AAC)
Lysine (Lys) (AAA, AAG)
Aspartic Acid (Asp) (GAU, GAC)
Glutamic Acid (Glu) (GAA, GAG)
Cysteine (Cys) (UGU, UGC)
Tryptophan (Trp) (UGG)
Arginine (Arg) (CGU, CGC, CGA, CGG, AGA, AGG)
Glycine (Gly) (GGU, GGC, GGA, GGG)
Isoleucine (Ile) (AUU, AUC, AUA)
Stop Codon (UAA, UAG, UGA)

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The chart for DNA codons is different from RNA, as it contains Thymine (which is known as Thymidine, when combined with deoxyribose) in place of Uracil (which is known as Uridine, when in combination with ribose). This DNA codon table is obtained by substituting 'T' in place of 'U' in the RNA codon table and is exactly identical to it. If you want to verify its correspondence with the RNA table, first substitute every T, with U.

Amino Acid / Start-Stop Codon Codon (Nucleotide Triplet Combinations)
Phenylalanine (Phe) (TTT, TTC)
Leucine (Leu) (TTA, TTG, CTT, CTC, CTA, CTG)
Methionine (Met) / Start Codon (ATG)
Valine (Val) (GTT, GTC, GTA, GTG)
Serine (Ser) (TCT, TCC, TCA, TCG, AGT, AGC)
Proline (Pro) (CCT, CCC, CCA, CCG)
Threonine (Thr) (ACT, ACC, ACA, ACG)
Alanine (Ala) (GCT, GCC, GCA, GCG)
Tyrosine (Tyr) (TAT, TAC)
Histidine (His) (CAT, CAC)
Glutamine (Gln) (CAA, CAG)
Asparagine (Asn) (AAT, AAC)
Lysine (Lys) (AAA, AAG)
Aspartic Acid (Asp) (GAT, GAC)
Glutamic Acid (Glu) (GAA, GAG)
Cysteine (Cys) (TGT, TGC)
Tryptophan (Trp) (TGG)
Arginine (Arg) (CGT, CGC, CGA, CGG, AGA, AGG)
Glycine (Gly) (GGT, GGC, GGA, GGG)
Isoleucine (Ile) (ATT, ATC, ATA)
Stop Codon (TAA, TAG, TGA)

Other than the two full sets of DNA, existent in every human body cell, there is an inherited genetic component, that is not contained in the cell nucleus, but resides in the mitochondria. In humans, mitochondrial DNA (mtDNA) is directly inherited from mother to son/daughter and is made up of about 16,600 nucleotide bases, and it encodes 37 genes. The codon translation in this organelle differs from the standard code slightly.

In the mammalian mitochondria, the AGA and AGG codons act as stop codons, instead of translating into Arginine. Also, AUA maps to Methionine in mtDNA, instead of Isoleucine, and the UGA codon translates into Tryptophan, instead of acting as a stop codon, as it normally does, in nuclear DNA.

These charts are useful references for anyone studying DNA transcription. Deciphering the genetic code is a tough job however. Scientists are in a stage now, where they have the entire human DNA sequence decoded, but most of it doesn't make sense. It is like having a printed book in your hand but not being able to read, as a lot of it sounds gibberish. There remains a lot more to be known in human genetics, as it is a vastly unexplored territory. This is good news for those of you, who are exploring this field as a career option.

Related Posts

A start codon is the starting point of translation in a cell. Read the following article to gain more information about this subject.

Stop codons are also known as nonsense codons, or termination codons. This article states all the facts regarding this particular type of codon.

All living organisms need energy to perform various functions. This energy is obtained by a process known as glycolysis. Scroll down to acquaint yourself with the process of anaerobic glycolysis.


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