Comments for Byte Size Biology http://bytesizebio.net The musings and ravings of a computational biologist about science, computers, music and, you know, stuff Fri, 03 Sep 2010 05:37:22 +0000 hourly 1 http://wordpress.org/?v=3.0.1 Comment on The open source spammer: extracting email addresses from an openoffice.org document by Martin Jambon http://bytesizebio.net/index.php/2010/09/01/the-open-source-spammer-extracting-email-addresses-from-an-openoffice-org-document/comment-page-1/#comment-1161 Martin Jambon Fri, 03 Sep 2010 05:37:22 +0000 http://bytesizebio.net/?p=4031#comment-1161 <code>strings</code> extracts printable ASCII substrings from any file. It's useful for files like .doc documents: <pre> strings foo.doc | egrep -o -i '\b[A-Z0-9._%+-]+@[A-Z0-9.-]+\.[A-Z]{2,4}\b' </pre> .docx documents are just compressed XML, so the following should work: <pre> unzip -c foo.docx | egrep -o -i '\b[A-Z0-9._%+-]+@[A-Z0-9.-]+\.[A-Z]{2,4}\b' </pre> <code>strings</code> is also handy for inspecting the bowels of a compiled executable: <pre> $ strings `which cat` /lib64/ld-linux-x86-64.so.2 __gmon_start__ libc.so.6 stpcpy ioctl stdout memmove getopt_long ... Written by %s, %s, %s, %s, %s, %s, %s, %s, and %s. Written by %s, %s, %s, %s, %s, %s, %s, %s, %s, and others. Copyright %s %d Free Software Foundation, Inc. %s: %s literal shell shell-always escape clocale memory exhausted ?P<@ @(NULL) 0 </pre> strings extracts printable ASCII substrings from any file. It’s useful for files like .doc documents:

strings foo.doc | egrep -o -i '\b[A-Z0-9._%+-]+@[A-Z0-9.-]+\.[A-Z]{2,4}\b'

.docx documents are just compressed XML, so the following should work:

unzip -c foo.docx | egrep -o -i '\b[A-Z0-9._%+-]+@[A-Z0-9.-]+\.[A-Z]{2,4}\b'

strings is also handy for inspecting the bowels of a compiled executable:

$ strings `which cat`
/lib64/ld-linux-x86-64.so.2
__gmon_start__
libc.so.6
stpcpy
ioctl
stdout
memmove
getopt_long
...
Written by %s, %s, %s,
%s, %s, %s, %s,
%s, and %s.
Written by %s, %s, %s,
%s, %s, %s, %s,
%s, %s, and others.
Copyright %s %d Free Software Foundation, Inc.
%s: %s
literal
shell
shell-always
escape
clocale
memory exhausted
?P< @
@(NULL)
                 0
]]> Comment on Changing directions by 96well http://bytesizebio.net/index.php/2010/09/02/changing-directions/comment-page-1/#comment-1159 96well Thu, 02 Sep 2010 22:54:32 +0000 http://bytesizebio.net/?p=4052#comment-1159 Wow! Simple and efficient. Wow! Simple and efficient.

]]> Comment on The open source spammer: extracting email addresses from an openoffice.org document by Iddo http://bytesizebio.net/index.php/2010/09/01/the-open-source-spammer-extracting-email-addresses-from-an-openoffice-org-document/comment-page-1/#comment-1155 Iddo Thu, 02 Sep 2010 14:32:43 +0000 http://bytesizebio.net/?p=4031#comment-1155 <a href="#comment-1154" rel="nofollow">@Martin Jambon </a> Thanks Martin, I never used strings... got an example one-liner using strings? @Martin Jambon
Thanks Martin, I never used strings… got an example one-liner using strings?

]]> Comment on The open source spammer: extracting email addresses from an openoffice.org document by Martin Jambon http://bytesizebio.net/index.php/2010/09/01/the-open-source-spammer-extracting-email-addresses-from-an-openoffice-org-document/comment-page-1/#comment-1154 Martin Jambon Thu, 02 Sep 2010 06:06:43 +0000 http://bytesizebio.net/?p=4031#comment-1154 "strings" is a really cool command for such purpose. “strings” is a really cool command for such purpose.

]]> Comment on When is it a good idea to cheat? by Wil http://bytesizebio.net/index.php/2010/08/27/when-is-it-a-good-idea-to-cheat/comment-page-1/#comment-1150 Wil Wed, 01 Sep 2010 22:11:29 +0000 http://bytesizebio.net/?p=3825#comment-1150 Nice article. A further comment on evolving cooperation: In order to explain emergence of cooperation in this context, you don't necessarily need kin selection. If you assume that, supported by geometric issues, different groups of various bacteria form, those groups with a healthy preference towards cooperation will grow faster and overtake areas with selfish, and therefore less performant mixtures. Nice article. A further comment on evolving cooperation: In order to explain emergence of cooperation in this context, you don’t necessarily need kin selection. If you assume that, supported by geometric issues, different groups of various bacteria form, those groups with a healthy preference towards cooperation will grow faster and overtake areas with selfish, and therefore less performant mixtures.

]]> Comment on 2010 Homology High-Low Count by Dan Gaston http://bytesizebio.net/index.php/2010/08/25/2010-homology-high-low-count/comment-page-1/#comment-1127 Dan Gaston Sun, 29 Aug 2010 22:10:36 +0000 http://bytesizebio.net/?p=3980#comment-1127 @Iddo I should have been clearer and realize I phrased it bad. They are only different semantically. What I meant is that I can see how people using the phrase distantly homologous could create confusion and lead to others to think of degrees of homology. My overall point though, is that the phrase distant homolog is widely used in molecular evolution circles and is, I feel, quite legitimate. Homolog and homology is still being used as a categorical statement. Either sequences are homologs or they are not. It would of course be more correct to say something like "evolutionarily distant homologs" but given the field the phrase is being used in, the evolutionarily part is understood and implied. @Iddo I should have been clearer and realize I phrased it bad. They are only different semantically. What I meant is that I can see how people using the phrase distantly homologous could create confusion and lead to others to think of degrees of homology.

My overall point though, is that the phrase distant homolog is widely used in molecular evolution circles and is, I feel, quite legitimate. Homolog and homology is still being used as a categorical statement. Either sequences are homologs or they are not. It would of course be more correct to say something like “evolutionarily distant homologs” but given the field the phrase is being used in, the evolutionarily part is understood and implied.

]]> Comment on I can’t hear you, the bacteria are too noisy by Iddo http://bytesizebio.net/index.php/2010/08/04/i-cant-hear-you-the-bacteria-are-too-noisy/comment-page-1/#comment-1126 Iddo Sun, 29 Aug 2010 20:22:25 +0000 http://bytesizebio.net/?p=3921#comment-1126 <a href="#comment-1124" rel="nofollow">@Lucas </a> Seems like the captcha in the blog carnival submission site is on the blink... so I cannot submit. You are welcome to submit it yourself, of course. And thanks! @Lucas
Seems like the captcha in the blog carnival submission site is on the blink… so I cannot submit. You are welcome to submit it yourself, of course. And thanks!

]]> Comment on 2010 Homology High-Low Count by Iddo http://bytesizebio.net/index.php/2010/08/25/2010-homology-high-low-count/comment-page-1/#comment-1125 Iddo Sun, 29 Aug 2010 20:13:42 +0000 http://bytesizebio.net/?p=3980#comment-1125 <a href="#comment-1118" rel="nofollow">@Dan Gaston </a> "Distant homologs" and "distantly homologous": I fail to see the difference, aside from semantics. <blockquote cite="#commentbody-1110"> <strong><a href="#comment-1110" rel="nofollow">brent</a> :</strong> <p>do you disagree with the use-case of “high homology” where it’s in reference to a syntenic region and not a single gene. e.g. “this region with 34 out of 55 genes retained as orthologs has a high (level of) homology”. i suspect that’s where at least a few of the “highly homologous” came from.</p> </blockquote> What's wrong with "(these chromosomal regions...) have a high fraction of homologous genes."? @Dan Gaston
“Distant homologs” and “distantly homologous”: I fail to see the difference, aside from semantics.

brent :

do you disagree with the use-case of “high homology” where it’s in reference to a syntenic region and not a single gene. e.g. “this region with 34 out of 55 genes retained as orthologs has a high (level of) homology”. i suspect that’s where at least a few of the “highly homologous” came from.

What’s wrong with “(these chromosomal regions…) have a high fraction of homologous genes.”?

]]> Comment on I can’t hear you, the bacteria are too noisy by Lucas http://bytesizebio.net/index.php/2010/08/04/i-cant-hear-you-the-bacteria-are-too-noisy/comment-page-1/#comment-1124 Lucas Sun, 29 Aug 2010 19:58:01 +0000 http://bytesizebio.net/?p=3921#comment-1124 One of the most fascinating pieces of work to come out last month! Maybe we will look back in a decade or so and be amazed that we ever thought mRNA levels were a good proxy for protein expression.. Coincidentally, this is also on of the clearest blogposts I read on the subject. Since I'm hosting next edition - would you consider submitting it to the Molbio Carnival (http://blogcarnival.com/bc/cprof_10473.html)? One of the most fascinating pieces of work to come out last month! Maybe we will look back in a decade or so and be amazed that we ever thought mRNA levels were a good proxy for protein expression..
Coincidentally, this is also on of the clearest blogposts I read on the subject. Since I’m hosting next edition – would you consider submitting it to the Molbio Carnival (http://blogcarnival.com/bc/cprof_10473.html)?

]]> Comment on 2010 Homology High-Low Count by Dan Gaston http://bytesizebio.net/index.php/2010/08/25/2010-homology-high-low-count/comment-page-1/#comment-1118 Dan Gaston Fri, 27 Aug 2010 01:11:51 +0000 http://bytesizebio.net/?p=3980#comment-1118 @Iddo: I still disagree. I agree that saying sequences are "distantly homologous" fits what you are describing, but at least in my area I don't see that. What I do see is the term "distant homologs". While the "distant" portion does, as you say, refer in some ways to the low percent identity of the homologs it is meant to refer to the evolutionary distance of the taxa. And those that I see use this commonly, including me, like you, harp frequently on the horrible use of phrases like more homologous, less homologous, percent homology, etc. I just don't think it is the same thing. @Iddo:

I still disagree. I agree that saying sequences are “distantly homologous” fits what you are describing, but at least in my area I don’t see that. What I do see is the term “distant homologs”. While the “distant” portion does, as you say, refer in some ways to the low percent identity of the homologs it is meant to refer to the evolutionary distance of the taxa.

And those that I see use this commonly, including me, like you, harp frequently on the horrible use of phrases like more homologous, less homologous, percent homology, etc. I just don’t think it is the same thing.

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