Bristol-Myers Squibb
Question
Asked 30th Oct, 2020
How can i annotate a eukaryotic genome (partial sequence ) ?
I want to annotate a eukaryotic partial genome sequence. Length around ~700 bp.
Is it possible using BioNumerics Or Genome Assembly! If Yes,then how?
Any suggestions will highly be appreciated!
Thanks in advance.
Most recent answer
Hello Dr. Anik Banik ,
I am not sure if you have RNA-Seq data. If you do then you can try out FINDER (https://github.com/sagnikbanerjee15/Finder). It is a gene annotator that uses RNA-Seq expression data to construct gene structures. It also generates predicted gene structures using BRAKER2 and can use protein sequences.
Thanks.
1 Recommendation
All Answers (16)
The University of Edinburgh
Hi Anik Banik if you are just looking for the gene that your 700bp region might fall in I would suggest just using BLAST, if you only want to do it once you can just copy and paste your sequence here: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
1 Recommendation
Sylhet Agricultural University
Hi, @Rishi
Thanks for your input. But i wanted to find out the Non-Coding Regio, CDS, 5/3UTRs etc.
Virginia Tech (Virginia Polytechnic Institute and State University)
Hi Anik Banik
Please check this :
1 Recommendation
Sylhet Agricultural University
Thank you so much for your suggestion @Vineet Upadhayay
1 Recommendation
University of Greifswald
You can try GeneMark-ES, or better, GeneMark-EP+. Also, there’s a script augustify.py in the AUGUSTUS repository on github. (Word of warning: success rate for annotation of foreign sequences with augustify is currently about 50%.)
2 Recommendations
Sylhet Agricultural University
Dear Dr. @Katharina Hoff,
Thank you so much for your valuable input.
1 Recommendation
University of Greifswald
I don’t recommend the BLAST approach unless you don’t care about the validity of a gene structure or you have sufficient experience to manually curate the gene structure. BLAST tells you s.th. about the locus but does not report valid gene structures including correct splice sites...
2 Recommendations
Brigham and Women's Hospital
Dear Anik,
I used this
for annotation.
What organism are you working on?
Thank you
Tamara
1 Recommendation
Sylhet Agricultural University
Dear Dr. @Tamara Salloum
Thank you for your input. Actually, I am working with an insect genome.
Anik Banik
1 Recommendation
University of New Mexico
Try GenSAS, an online genome annotation server https://www.gensas.org/user?destination=/gensas
1 Recommendation
Sylhet Agricultural University
Dear Dr. Lijing Bu,
Thank you very much for your valuable input.
-Anik Banik
1 Recommendation
Julius Kühn-Institut
Another possiblitiy can be found on http://www.softberry.com/ . On this webpage you find valuable tools for gene prediction (model orgnaisms available). For only one gene you can try annotation of animal or plant genomes (http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfind). Quit simple the resulting coding sequences can be blasted after ab initio identification.
1 Recommendation
Sylhet Agricultural University
Dear Dr. @Thomas Wolfgang Wohner,
Thank you so much for your valuable input.
1 Recommendation
Bristol-Myers Squibb
Hello Dr. Anik Banik ,
I am not sure if you have RNA-Seq data. If you do then you can try out FINDER (https://github.com/sagnikbanerjee15/Finder). It is a gene annotator that uses RNA-Seq expression data to construct gene structures. It also generates predicted gene structures using BRAKER2 and can use protein sequences.
Thanks.
1 Recommendation
Similar questions and discussions
Megalodon is hostage to an anthropomorphic interpretation hyper iconic-metaphorical of the fossil remains (strong allometry & heterochrony)??
𒅌 Megalodon is hostage to an anthropomorphic interpretation hyper iconic-metaphorical of the fossil remains?? Is this a shark that has been subject to strong allometry & heterochrony phenomena??
The Megalodon (Otodus megalodon: Paleocene-Pliocene, 66-2.5 Million Years Aug) is certainly the best famous shark together with the large white shark.
However, the fact is immediately striking (in the current state of data: October 2023) that the skeleton of this group of species (O.obliquus, O.aksuaticus, O.auriculatus, O.sokolovi, O.angustidens, O.chubutensis, O.megalodon) is almost missing, especially for the most massive species, if except for the giant teeth and very few vertebral elements.
Therefore the reconstruction, although truthful and compatible with the current sharks of the same taxon (Lamniforms), is based purely on a reconstruction which does not take any alternative hypotheses into account.
Hypothesis that exclude any morphological bizarre; oddities very common, however, in today's zoological practice (see: Regalecus; Psychrolutes; Lophiiiforms; Chlamydoselachus; Helicoprion✟; Chimaera; Edestidae✟; Mitsukurine; Isistius; Megachasma;..).
Given that the current hypothesis on the morphology of Megalodon (a colossal "white"-shark) is correct, what could be the plausible alternatives that would deserve to be taken into consideration?
The thesis that will be exhibited was born over 10 years ago (about 2010) and is based / was based on some points:
--lack of fossil remains that perfectly justified the typical morphology of a colossal "white"-shark;
--presence of numerous phenomena between sharks and other Chondrichthyes, of absolutely out of standard morphology;
--not consideration of ontogenetic phenomena that can lead to radical and extreme morphology;
--enormous cost of being an active predator and as well as colossal dimensions;
--an ecological role with low or very low levels of sustainability (easy prey to competitors** superior both in morpho-physiology and in behavior);
--trophic niche of ""vertical migratory scavenger"" not considered.
___________________________________________________________________
**Zygophyseter_varolai: Miocene (~7 million years ago), 10m lt.
**Orcinus: Miocene-Holocene (~11 million years ago until now), 5-9m lt.
**Ankylorhiza: Oligocene (~29-23 million years ago), 5-6m lt.
**Basilosauridae: Eocene-Oligocene (~41-28 million years ago), 6-17m lt.
___________________________________________________________________
The thesis is the following.
Like all abyssal fish, Megalodon was equipped with a huge mouth accompanied by hyper-trophic teeth.
From 1/2 to 1/4 of the entire volume and/or body mass, belonged precisely to the head-gill region.
The body, posterior to the gill area, was strongly snake-shaped, and with strongly decreasing diameters from the gill region up to the end of the tail.
The snake-shaped body appeared almost atrophied compared to the head, which had undergone heavy effects of allometry & heterochrony, completely similar to those of the abyssal Lophiiiforms and Chimaera.
Its life cycle was not permanently abyssal, but regular vertical migration (even over 1-2 km) were carried out in the ocean column; migrations that could be determined by food and/or reproductive phenomena (see Regalecus).
Therefore its food habitus was characterized by both active predation (similar to that carried out by Lophiiiforms) and necrophagy on large animals.
It cannot be ruled out that Megalodon suffered predation from much more active species, some of which were previously** listed.
This thesis is plausible?
At present, it should be considered as worthy of in-depth study, in order to strengthen the thesis of the active super-predator similar to a colossal "white" shark.
An interesting example of allometric-heterochronic phenomena associated with a very particular morphology is the megamouth shark..
.. https://www.ndtv.com/world-news/rare-megamouth-shark-washes-up-on-beach-in-the-philippines-3084080
𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂
𒅌 Il Megalodonte è ostaggio di una interpretazione antropomorfica iper iconico-metaforica dei resti fossili?? Si tratta di uno squalo che è stato soggetto a forti fenomeni di allometria & heterochrony??
Il Megalodonte (Otodus megalodon: Paleocene-Pliocene, 66-2,5 million years ago) è certamente il più noto squalo unitamente al grande squalo bianco.
Colpisce subito il fatto (allo stato attuale dei dati: ottobre 2023) che lo scheletro di questo gruppo di specie (O.obliquus, O.aksuaticus, O.auriculatus, O.sokolovi, O.angustidens, O.chubutensis, O.megalodon) è pressoché mancante soprattutto per le specie più cospicue, se fatta eccezione per i denti giganti e pochissimi elementi vertebrali.
Pertanto la ricostruzione, pur se veritiera e compatibile con gli attuali squali del medesimo taxon (Lamniformes), è basata puramente su una ricostruzione che non tiene minimamente conto ipotesi alternative.
Ipotesi che escludono qualsiasi bizzarria morfologica; bizzarrie comunissime però nella pratica zoologica odierna (vedi: Regalecus; Psychrolutes; Lophiiformes; Chlamydoselachus; Helicoprion✟; Chimaera; Edestidae✟; Mitsukurina; Isistius; Megachasma;..).
Dato per scontato che la ipotesi attuale sulla morfologia del Megalodonte (uno squalo ""bianco"" colossale) sia corretta, quali potrebbero essere le alternative plausibili che meriterebbero di essere prese in considerazione??
La tesi che verrà esposta, nacque oltre 10 anni fa (circa 2010) e si basa/basava su alcuni punti:
--mancanza di resti fossili che giustificassero perfettamente la morfologia tipica dello squalo bianco;
--presenza di numerosissimi fenomeni tra gli squali e altri condritti, di morfologie assolutamente fuori standard;
--non considerazione di fenomeni ontogenetici che possano portare a morfologie radicale ed estreme;
--enorme costo di essere un predatore attivo e dalle dimensioni oltre che colossali;
--ruolo ecologico con bassi o bassissimi livelli di sostenibilità (facile preda di competitors** superiori sia nella morfo-fisiologia sia nel comportamento);
--nicchia trofica di ""spazzino migratore verticale"" non considerata.
___________________________________________________________________
**Zygophyseter_varolai: Miocene (~7 million years ago), 10m lt.
**Orcinus: Miocene-Holocene (~11 million years ago until now), 5-9m lt.
**Ankylorhiza: Oligocene (~29-23 million years ago), 5-6m lt.
**Basilosauridae: Eocene-Oligocene (~41-28 million years ago), 6-17m lt.
___________________________________________________________________
La tesi è la seguente.
Come tutti i pesci abissali, il Megalodonte era dotato di una enorme bocca corredata da denti ipertrofici.
Da 1/2 ad 1/4 dell'intero volume e/o massa corporea apparteneva proprio alla regione capo-branchie.
Il corpo, posteriormente alla zona branchiale, era fortemente serpentiforme e con diametri fortemente decrescenti proprio dalla regione branchiale fino alla estremità della coda.
Il corpo serpentiforme appariva quasi atrofico rispetto al capo, il quale aveva subito pesantissimi effetti di allometria & heterochrony del tutto similari a quelli dei lofiformi abissali, delle chimere.
Il suo ciclo vitale non era permanentemente abissale ma venivano effettuate regolari migrazioni verticali (anche oltre 1-2 km) nella colonna oceanica; migrazioni che potrebbero essere determinate da fenomeni alimentari e/o riproduttivi (vedasi Regalecus).
Pertanto il suo habitus alimentare era caratterizzato sia da attiva predazione (analoga a quella svolta dai Lophiiformes) sia da necrofagia su animali di grande taglia.
Non è da escludere che Megalodon subisse la predazione da specie molto più attive, alcune delle quali precedentemente elencate.
Questa tesi è plausibile??
Allo stato attuale dovrebbe essere ritenuta come meritevole di approfondimento-indagine, al fine di rafforzare la tesi del super-predatore attivo simile ad un squalo ""bianco"" colossale.
Un esempio interessante di fenomeno allometrici-eterocronici associati ad una morfologia molto particolare è lo squalo megamouth..
𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂
𒅌 ALLOMETRY & HETEROCHRONY 𒅌
Allometry is the study of the relationship between the size of the body with form, anatomy, physiology and behavior. Allometry has well known practical applications for the investigations on differential growth rates of the body parts of a living organism. The mathematical models below allometry studies are based on the exponentials.
In evolutionary developmental biology, heterochrony is any genetically controlled difference in the timing, rate, or duration of a developmental process in an organism compared to its ancestors or other organisms. This leads to changes in the size, shape, characteristics and even presence of certain organs and features. It is contrasted with heterotopy, a change in spatial positioning of some process in the embryo, which can also create morphological innovation. Heterochrony can be divided into intra-specific heterochrony, variation within a species, and inter-specific heterochrony, phylogenetic variation, i.e. variation of a descendant species with respect to an ancestral species..
𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂𒁂
𒅌 BIBLIOGRAPHY 𒅌
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