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Jan
29
comment Question about SAM CIGAR string
Don't know how to quote properly in a comment. I quoted footnote 10 of the current sam format specification (page 7).
Jan
29
comment Question about SAM CIGAR string
The MD optional flag gives more details regarding the alignment: > The MD field aims to achieve SNP/indel calling without looking at the reference. For example, a string ‘10A5^AC6’ means from the leftmost reference base in the alignment, there are 10 matches followed by an A on the reference which is different from the aligned read base; the next 5 reference bases are matches followed by a 2bp deletion from the reference; the deleted sequence is AC; the last 6 bases are matches. The MD field ought to match the CIGAR string.
Nov
18
comment What is this dried animal for sale?
I'd guess it's a primate, or a big rodent.
Nov
17
comment Does a DNA sequence has its own derivation tree or pattern?
There are regulatory motif databases, and prediction algorithms for functions in a sequence, but all this is not fully known. Indeed, things are rarely fully regular in biology, so every bioinformatics predictions ideally should be completed with experimental confirmation. Also, the same sequence can sometimes be parsed in various way: a single DNA sequence may encode several proteins, depending on which portions are actually translated into amino-acids. Some keywords you may be interested in: start codon, stop codon, open reading frame, 3'UTR, 5'UTR, binding box.
Nov
4
comment What plant is this?
True, it could also be an Asteraceae, but the texture of the yellow part, the low number and the almost-round shape of the white petal-like parts somehow make me prefer the other hypotheses.
Oct
13
comment What sort of seed pod is this?
Are there any trace of a hole through which a bug could have entered? The content looks messy. Can you isolate seed ?
Oct
12
comment What happened to this seashell?
I'd say that the holes were made by animals. I know some mollusks can make holes on rocks, for instance en.wikipedia.org/wiki/Pholadidae But in the case of this shell, the animals must be much smaller.
Sep
9
comment What is the name of the plant with the down-falling light purple leaves?
The common name in English is "foxglove". Note that they are poisonous.
Jul
15
comment Can someone identify this stinging plant?
It would help if you could add in what country you mother was stung by this plant.
Jul
6
comment Help identify this worm-like thing
Are leeches supposed to like bacon ? I thought they needed fresh blood.
Jul
2
comment What is the name of this bird?
Couldn't it be a juvenile of some well known species ?
Apr
24
comment I have a black tiny bug crawling all over the house
It seems from some of the photos that the "stage 2" have quite thin and long antennae, unlike what I've seen in termite images. Besides, the size is very small, so I wouldn't bet they are termites.
Apr
24
comment I have a black tiny bug crawling all over the house
Can you keep some "stage 1" isolated in a jar with some dust and a tiny drop of water (just guessing what they might feed on) and see if they actually turn into "stage 2" ?
Apr
24
comment I have a black tiny bug crawling all over the house
You write: "once i found a very little few under the carpet but it generally stays away from the carpets and stays on the tiles". Could it be that they are simply less visible when in the carpet as when on the tiles ?
Mar
25
comment Sequence compression method / format
Note that block compression can be applied to any type of file, including fastq or fasta, using the bgzip utility that comes with samtools. That said, I don't know to what point this makes the file more easy to deal with than just using plain gzip. Biopython has some degree of support for bgzip.
Mar
20
comment Identifying internal structures of dissected fish
A swim bladder in two parts is a common thing. At least I remember having seen at least in some of the few fish dissection I've made.
Sep
17
comment How closely related are two parasites Giardia intestinalis and Trichomonas vaginalis?
Be careful though that Tolweb is not always very up-to-date.
Sep
9
comment Is this a grackle with an unusually long decurved bill (Phoenix AZ, USA)
Could it be that the bird was holding something into its beak, which made it look curved?
Aug
19
comment How do I perform recurring pattern mining or regular expressions of nucleotide sequences?
For python, the Bio.motifs package from BioPython could be useful: biopython.org/DIST/docs/tutorial/Tutorial.html#sec244
Dec
5
comment Cats, Dogs and Bears - how are they related?
What do you mean by "paralogous clade"?