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Questions tagged [homology]

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Does diamond tblastn exist?

I actually want to use diamond instead of blast because it is faster with small sequences and big genomes, but I actually want to make a tblastn with several protein sequences as queries and the ...
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1answer
52 views

Gene vs Protein homology

I am trying to find homologs for some proteins and I am wondering if it is better to find it by comparing the proteins or the coding genes or either is fine.
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Is there any evidence of homologous somatic pairing in taxa aside from Dipterans and budding yeasts?

Homologous somatic pairing is the physical colocation and pairing of the paternal and maternal chromosomes in a cell during growth phases of a cell. This is interesting as most taxa that we know about ...
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54 views

Homology modelling of protein with two identical subunits in its quaternary structure

I am using homology modelling to assign the 3D structure of Torpedo acetylcholine receptor (Unwin 2004, 2bg9 in RCSB) to human muscle nAChR. The problem is, both Torpedo receptor, and human receptor ...
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42 views

Does homology of a trait necessarily imply that the most recent common ancestor had the trait?

If two different species have a trait that is homologous, does this mean that the most recent common ancestor necessarily had the same trait?
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117 views

Can two proteins sharing a few domains be considered homologous?

I wonder when to say two proteins are homolog. In the current example I checked the sequence of these two proteins in pfam and as you see they have some shared domains but all domains are not shared. ...
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1answer
48 views

Gene copies vs. gene paralogs - what's the difference?

I'm trying to get into the theory and practice of gene copy number variation (CNV) analysis, but there is something basic confusing me, which I couldn't yet figure out. Sorry if this is a dumb/trivial ...
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1answer
23 views

tissue-specific expression of homolog genes

Two or more genes are homolog if thay have similar sequences. homolog sequences between species are called orthologs (caused by speciation events) and homolog sequences in an species are called ...
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99 views

Finding phylogenetic distance between sequences?

I'm working on a piece of software that does comparative genomic analysis; and I found out in homology methods for functional annotation, it's preferable to pick the high scoring homolog from a ...
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137 views

What are some examples of non-homologous sequences having similar functions?

I am trying to find some proteins that are non-homologous but functionally similar. However, I cannot seem to find concrete examples. Can someone please point out any resources or provide examples?
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2answers
2k views

Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits?

My question is contextualised for basic phylogeny knowledge. Here is my understanding: similar or identical traits between any two species, at the basic level, can be either homologous, meaning the ...
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32 views

When to decide that two similar sequences are different genes or not?

Working on RNA-Seq data directed me to ask this question. In RNA-Seq jobs, after de novo assembly we have lots of transcripts with different rates of similarity (0 to almost 100 percent) that we ...
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1answer
311 views

Identity and similarity for Multiple Sequence Alignment (MSA) of proteins

I have to do homology modeling for a transmembrane protein (sodium channel) and right now I am in the process of aligning the sequences of the template with the homologous proteins I have found. I am ...
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How large is the range of 'same origin' when determining whether two organs are analogous or homologous?

The pectoral fins of a whale and a shark. Are they analogous organs? I was looking at this question, and I saw that the two answers defined the range of 'same origin' differently. One said that sharks ...
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2answers
3k views

The pectoral fins of a whale and a shark. Are they analogous organs?

Analogous organs: Different origin, same functions, Homologous organs: Same origin, different functions but same main structure// right? So, what is the case for the pectoral fins of a shark and a ...
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1answer
2k views

When was the last common ancestor of pig and human?

Some religions regard pigs as unclean on the grounds that pig flesh is closest in composition to human flesh. I don't believe this for one instant, but it got me thinking, just how close is pig and ...
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NCBI EUtils. Get Homolog infromation using Gene ID

How to retrieve homologs information in xml or json format from NCBI using gene ID? I tried one URL: ...
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2answers
154 views

Do the bacterial species X, Y, Z code for proteins A, B, C?

My PI has assigned me a task to gather evidence to determine whether or not a list of particular species of Campylobacter and Helicobacter code for a list of several proteins. To put it simply I’ve ...
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2answers
12k views

How do other primates treat their fingernails?

Do all primates have to trim their fingernails in some way, or do some primates' fingernails wear off through natural use? Also, is constant nail growth common to all primates?
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100 views

Homology ratio comparison between different species

I found the following homology ratio: protein coding genes of the organism with an homolog in mouse / all protein coding genes in the organism I have done this for all protein coding genes between ...
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1answer
9k views

What do the Clustal Alignment Symbols Mean?

Occasionally I will run protein alignments on peptide families and I can never remember what the symbols mean to show degrees of identity. What do they mean?
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Are there any good reviews on the mouse and human conservation in coding and gene regulatory module regions?

I was looking for reviews that deal with conservation between mouse and human of proteins, noncoding RNAs, gene regulatory module (such as promoters and enhancers), gene regulatory networks post the ...
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4answers
803 views

Is there a PSI-BLAST for nucleotide sequences?

I understand that one can translate a nucleotide sequence and run PSI-BLAST on the protein (proteins if you take the 6 reading frames), but I'm looking for distant homology for bacterial small RNAs (...
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188 views

What are the statistical tools for distinguishing molecular analogy from homology?

Scientists have developed statistical tools that distinguish "distant" homologies from coincidental molecular homoplasy in extremely divergent sequences. What are these tools?How are they used ? I ...
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262 views

Paralogous genes in genome-wide association studies?

Has anybody tested if paralogous genes are over-represented among the genes identified by genome-wide association studies (GWAS)? For example, if a GWAS study finds 200 genes associated to the ...
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365 views

Homologies to insect wings

All winged vertebrates have wings which are homologous to each other and to the forelimbs of the non-winged vertebrates. But what about insect wings? Are all insect wings homologous, and are there any ...