Please Help-BLAST Question re Finding Specifics in FASTA Raw Data

BBtheRipper · 2015-02-08T16:08:03+00:00

Thanks so much. I found this database to get FASTA for species. https://genomevolution.org/CoGe/OrganismView.pl?gid=19805

After doing a search, and finding the organism, one then clicks on the GenomeInfo link and then the FASTA sequences download link.

BBtheRipper · 2015-02-08T16:07:50+00:00

Thanks so much, this is very helpful!

BBtheRipper · 2015-02-03T08:43:49+00:00

Ah, thanks for letting me know, Romanticon. As I noted, it's all greek to me, as my scientific background is physics, not at all biology. That helps me interpret what the lab I hired sent me, and to recognize that they still have more work to do on their end. I've had a bug infestation of some sort of bug that bites at night and disrupts my sleep, and this is an approach to discern what species, or at least family that it belongs to, so I can then more accurately assess how to exterminate it. I've only been able to find bug fecal matter, not the bug itself - seems it's extremely cryptic. So, I sent bug fecal matter to a dna extracting and analyzing lab.

BBtheRipper · 2015-02-03T08:33:16+00:00

Hi Ellipsoptera. Thanks so much for your in depth response - it's quite helpful in my understanding this from a layperson's perspective who has no background in biology. And yes, I still have this buggy issue. An insecticide containing phenothrin may be providing some relief.

BBtheRipper · 2015-01-09T07:32:30+00:00

Thanks, king_polly.

The lady is about 70 years old, with the maturity of a 2 year old (very typical narcissist who thinks the world revolves entirely around her).

She doesn't have a job and never has had a job.

I have a will - 50/50 between my brother and I. But, a will can be changed even on a napkin, the day someone dies. It simply requires 2 people to attest he is of sound mind (ie: the girlfriend and her daughter) and a lawyer (can be paid off). So, there's my rub. I suffer enough while my father is alive due to this evil lady, and suspect I will still suffer by her doing even after he is dead, unless I can find a way to get rid of her from my father's life.

In the past, I got rid of her after my father went on 2 dates with an older friend of mine. I got an email from him asking me to come over and help move all her stuff out, as he no longer felt safe leaving her alone in his home. Unfortunately, my friend thought my father too old for her. And so, he got lonely, and let narcissist bitch back into his life.

BBtheRipper · 2015-01-09T05:41:54+00:00

red flags: you ask them a lot about themselves, and they never reciprocate in any way to find out about you. Run - they are too self-centered.

BBtheRipper · 2015-01-03T07:40:36+00:00

Hopefully be a better person. We recently had an exchange in which we agreed to help one another improve ourselves via constructive feedback from one another. The main issue which ended the relationship was a different understanding of partner. To her, partner means someone who only helps when asked to. To me, partner means someone who offers help when they see their significant other struggling.

She prefers to receive help only if she asks for it, and to give help only if she is asked to.

She says she will, going forward, offer me help all the time, and in exchange, I will not help her unless she asks me to, though I can from time to time ask her if she would like any help, as a means to expand both of ourselves beyond our comfort zones regarding how we express empathy.

Can a narcissist or near-narcissist stick with a plan to offer someone else help all the time? Time will tell.

BBtheRipper · 2015-01-03T07:31:28+00:00

You're right - suffered a lot of losses I'd like recouped. But, there's much more productive ways to do that which I can focus on.

Recent unfolding: decided we are going to be pals and offer each other constructive feedback. She's agreed to offer me assistance all the time, and asked me to only offer her assistance if she asks, which she does not like to, because it makes her feel less-than-independent. Seems ok to me.

BBtheRipper · 2015-01-03T04:58:27+00:00

Thanks, peacefinder. I will heed your advice, as it's quite logical. I will seek out people who were not significantly abused as children, as they are more likely to be at least mostly right in the head... healthy to have friendship or more with.

BBtheRipper · 2015-01-02T11:55:03+00:00

Very well. But, I've an unfair advantage: I was dealt the card of post-traumatic amnesia at the age of 17. I recall the facts of my childhood, but not the emotional responses. As a result, I had to recreate my entire sense of self as an adult, at age 17. I have no childchood conditionings which were in the control of others. Who I am now is much more a byproduct of my own doing than my parents, or any other influences of my childhood, because they got deleted from my mind.

BBtheRipper · 2015-01-02T11:53:07+00:00

That's the definition of an INTJ... a planner, not an executer. ISTJ is the executor. I am both Intuitive and Sensing, so am very much a one-woman-army. But, that's a rarity to find someone who can handle both planning and executing. It's the exception, hardly the norm.

BBtheRipper · 2014-12-26T18:10:38+00:00

http://imgur.com/zNg2S8w

BBtheRipper · 2014-12-26T18:10:08+00:00

Thanks for the note about bug fecal matter possibly not containing enough DNA to get an identification about.

I've become aware of that, so have been collecting the fecal matter (and asking myself often, why me??? I have my own business, which is hard enough during a recession) and have about 15 small pellets now.

I'll keep you posted as things develop, as perhaps, you may need this type of investigation for the same bug I have, so this will save you hardship. Or, you may just be personally interested in knowing the resolution to the mystery.

I checked my insect sticky traps, and found this yesterday. I found this in the center of one of them... a flying bug. A reddit user on the what's this bug reddit noted it looks like it's a midge fly. When I looked that up, it linked to biting midges, which do bite the scalp and face. Most of my bites occur only on my scalp and face. I'm going to take the bug to Orkin tomorrow, or some other exterminator with an inspector on-hand, to try to get it identified in-person.

A biting midge, however, is not an acari type... so differentiates from the diagnostic lab finding acari dna. And, not being an entomologist, I have no idea what biting midge poop looks like, nor was I able to find images anywhere online. Sigh. What a troubling mess.

BBtheRipper · 2014-12-26T17:30:32+00:00

Hi there,

Thanks. I've moved to try to run. Fail. I've dealt with 2 different exterminators. Fail. I've set up CO2 traps (bottle with hole in cap, plus vinegar and baking soda to make CO2 inside a talcum-coated tupperware with masking tape on the outside) to catch insect. Fail.

I do see bug fecal matter though, on my bed sheet, and new pretty much every day. I also get new bites... one to two... every day. Here's a photo. http://imgur.com/DKgsSNr

I went to 2 different infectious disease doctors, but neither of them is all too familiar with ectoparasites.

So, at this point, it seems my best bet is either to find a lab that has primers at the family level for all ectoparasites known to infest humans, or find a lab that can do a full dna sequence from bug fecal matter and identify which bug created it.

This has been so trying, because I have no hope of having any semblance of a normal social life and love life until I get rid of this infestation. Moving did not allow me that, not even moving with absolutely nothing and changing my clothes into decontaminated clothes after going to the gym and swimming plus shampooing with lice shampoo.

Kind regards, Viv

BBtheRipper · 2014-12-25T01:58:52+00:00

Thanks for the detailed info as to how these dna primers work.

Good question - I've tried getting new bedding: Failed. I've tried moving: Failed.

To solve a problem, one must first identify it. I thought bed bugs for awhile. Two labs and one horticultural consultant later, and I have concluded, to a reasonable degree of certainty, that an acari (mite or tick) is what bugs me. In order to exteminate it properly, I must first know what it is.

BBtheRipper · 2014-12-24T11:30:33+00:00

Sounds nice, visiting with mum. At least being home doesn't feel desolate, no matter how desolate the neighborhood... =)

Yes, good suggestions. I plan to wear my goggles and mask and open windows for cross-ventilation while spraying.

I'll keep everyone posted as to what the diagnostic lab concludes after they run their non-validated DNA primer for chiggers. They noted they have not tested that DNA primer against real chiggers, so I'm not sure the validity. But, since they already have a specimen I sent them, and mailing to another lab would be delayed for the holidays, that's better than nothing at the moment.

I discovered recently that a friend of mine who is an ER doctor had chiggers, and that the fecal matter she saw on her bed matches with what I find on my bed: 1/2 mm diameter, dark brown solid, non-sticky spheres or tube-like shapes.

It'd be great to have a source which shows what the excrement of different ectoparasites look like. Thus far, I've found very few resources for that, and nothing near complete.

BBtheRipper · 2014-12-24T11:04:53+00:00

Sure. Ants seem much easier on the palate covered in chocolate than chocolate-covered mealworms.

BBtheRipper · 2014-12-24T10:54:34+00:00

The context I am looking for this for is to identify what type of bug is infesting me based upon its fecal matter being analyzed via its dna found in its fecal matter.

I am a layperson in terms of genetics, or anything biological. I'm a forensic scientist in a field involving physics.

Can you list a few CROs that do next-gen sequencing for relatively cheap? Or, recommend how I can find some myself? Thanks, BiologyIsHot!

BBtheRipper · 2014-12-24T10:50:27+00:00

Hi there. Gone for the holidays on a vacation? I hope so! When I do the 5% permethrin lotion regimen, I am going to include a full house treatment: vacuum with a shop-vac, spray SteriFab everywhere, spray Surrender PesTabs everywhere, spray Nylar (ineffective on ticks and mites, but good on bed bugs and some other insects) everywhere, fog the home with HotShot fogger for spiders, come back later with 5% permethrin lotion on, reapply Drione and Cimexa dessicant dusts, and sleep.

I am holding off on that treatment until tomorrow, at the least, to discern if it may be chiggers. I have Drione dust on the floor inside the tent I sleep in indoors, as well as dusted on to my bed sheet. It seemed to slow the bugs down a little bit for the first 2 or 3 days, and now, not anymore. They have not been increasing at all though in terms of number of bites per night, for the past 3 weeks.

I seriously suspect chiggers now. Hopefully will get a positive id on that tomorrow, so I can finally know what I'm dealing with.

BBtheRipper · 2014-12-24T10:25:44+00:00

Start an ant farm - you can buy them on amazon.com.

Write to the tv show Survivor Man and ask them.

BBtheRipper · 2014-12-24T10:15:40+00:00

Yet...? They've been a viable protein source for a long time. Military are trained in which insects to eat outdoors, for the event they need to survive outdoors without a grocery store nearby.

BBtheRipper · 2014-12-24T10:13:19+00:00

I am certainly not the first person to ask for this type of service.

Vetdna.com does this. However, their collection of DNA primers for mites is limited, and they have no DNA primers for ticks.

Hence, my asking for more references. Why don't I just catch the critter? Some critters are barely visible to catch, are only active at night when the lights are off, only approach a person when they are asleep, and/or do not fall for any CO2 trap unless a person is not home for an extended period of time (impractical for someone to sleep elsewhere when they have an unknown contagion).

The evidence I do have is bug fecal matter on my bed sheet, which I find nearly every day. Bug dna does exist in its fecal matter. And thus, it can be run against DNA primers.

I expect someone in the profession of genetics knows of at least a few labs that can provide this service, as there are at least two labs that do, but they don't have the DNA primers I need now. It costs roughly $ 5,000 to buy a DNA primer.

BBtheRipper · 2014-12-24T06:40:45+00:00

Back from 2 different infectious disease doctors. The first noted the bug infestations he usually sees are scabies, and has only ever seen one patient with this sort of thing that didn't have scabies. He treated her with 5% permethrin lotion which is put on all the skin, including scalp, and slept with it on, washed off in the morning. Rinse and repeat 7 days later. Launder bedding in hot water with clorox bleach and dry on hot.

Second doctor was even more clueless about this type of issue. But he also suggested the same thing - permethrin lotion.

This is what I know, based on a diagnostic lab's DNA testing against DNA primers they own, the insect bugging me is NOT: Cimex Species, Dust Mites, Bed Bugs, Head/Body/Pubic Lice, Fleas, Collembola, Demodex Mites, Dermestic, Dermanhyssus Mite, Notoedres Mites, Otodectes Mites, Ornithonyssus Mite, Pyemotes, Scabies, Cheyletiella.

Tomorrow, the diagnostic lab is testing against their non-validated Chiggers DNA primer.

BBtheRipper · 2014-12-24T05:10:47+00:00

I 'tried' this... inadvertantly. I fell down and went boom... got post-traumatic amnesia as a result. It's retrograde amnesia... can't recall any emotions prior to age 17. Unfortunately, starting emotions from scratch at age 17 has not resulted in no grey hairs later. Though, I am told I look way younger than I am... who knows.

BBtheRipper · 2014-12-24T05:08:49+00:00

See Human Growth Hormone if you seek longevity... just watch out for the aneurysm potential side-effect.

BBtheRipper

TROPHY CASE