[Bioperl-l] The Feature changes which have broken compatibility

Hilmar Lapp hlapp at gmx.net
Wed Feb 2 13:03:45 EST 2005


I'm guess nobody will be surprised, but I do agree with Jason's 
sentiment wholeheartedly.

	-hilmar

On Wednesday, February 2, 2005, at 05:16  AM, Jason Stajich wrote:

>
> This whole changing of core SeqFeature::Generic objects is pretty 
> disturbing.
>
> Why can't we do this:
> - Bio::SeqIO, Bio::Tools::GFF, Bio::SeqFeature::Generic all remain the 
> same as they were in 1.4.  We back out the major changes to the 
> inheritance - figure out whether or not things should be 
> Bio::AnnotatableI.
>
> - Bio::FeatureIO make Bio::SeqFeature::Annotations which can have 
> whatever interface and remove the "features your find annoying" 
> without breaking the existing code which relied on things.
>
> The burden is on the person implementing new code NOT to break the 
> existing interface which we want to be backwards compatible unless 
> there is some reason not to.....   There is no good reason scripts 
> that work with bioperl-1.4 can't work with 1.5 (or 1.6).
>
> Many people will continue to use Bio;:Tools::GFF - for those who want 
> GFF3 and SO validation, they should use Bio::FeatureIO.  Lots of 
> people are happy to continue in their blissful state of not using SO 
> (and not installing Graph::Directed in order to parse a genbank file).
>
> The fact that Bio::SeqIO really expected Bio::SeqFeature::Generic 
> objects instead of Bio::SeqFeatureI objects probably meant that we 
> should be updating Bio::SeqFeatureI interface not just breaking 
> things.  We might need to improve Bio::SeqIO/Bio::SeqFeatureI to 
> insure Bio::SeqFeatureI is general enough for the two objects.
>
>
> It really makes me uncomfortable how sloppy this appears to people 
> using the toolkit - many of us have worked really hard to maintain 
> backwards compatibility - dealing with the "annoying features" and 
> somewhat legacy function names because someone wrote them before us 
> and we didn't want to break people's scripts.   When making lots of 
> changes they really need to be either well tested (with additional 
> tests perhaps) OR they need to be insulated from existing code.
>
> I really think we need to branch and back out these changes so we can 
> provide a 1.5.1 release which most of the API is compatible with 1.4 
> scripts, and potentially plan to release 1.6 off this branch.  I 
> cannot be the release master, someone else must step up to be the 
> coordinator and help with QA.
>
> -jason
>
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
> On Feb 2, 2005, at 5:52 AM, Marc Logghe wrote:
>
>> Allright, status update about my little 'gbrowse on top of 
>> biosql'-project.
>>
>> I have prepared a fresh linux box with bioperl-live tagged 
>> bioperl-release-1-5-0, bioperl-db and bioperl-schema HEAD, 
>> release_1_62-bugfixes Generic-Genome-Browser.
>> I loaded some genbank proteins in biosql (Thanks Hilmar for helping 
>> me out !) and adapted 06.biosql.conf.
>> Three observations that at this (early) point can be made:
>> 1) init_code (providing some missing methods in order to make 
>> Bio::SeqFeature::Generic and Bio::Graphics::Feature more compliant) 
>> is not needed anymore, which is good (Thanks Lincoln)
>> 2) all features are displayed in duplicate (I'll flesh that one out). 
>> This confirms the things Genevieve is seeing.
>> 3) Bio::SeqFeature::Generic::get_tag_values does not exist anymore: 
>> Bio::SeqFeature::Geneneric does not inherit from Bio::AnnotatableI 
>> which implements that method, which is bad (can it pass the tests, 
>> then ?). I don't know what the situation is in bioperl-live HEAD.
>>
>> Cheers,
>> Marc
>>
>>
>>> -----Original Message-----
>>> From: gmod-gbrowse-admin at lists.sourceforge.net
>>> [mailto:gmod-gbrowse-admin at lists.sourceforge.net]On Behalf Of
>>> Genevieve
>>> DeClerck
>>> Sent: Tuesday, February 01, 2005 10:57 PM
>>> To: gmod-gbrowse at lists.sourceforge.net
>>> Cc: Lincoln Stein
>>> Subject: Re: [Gmod-gbrowse] features not displaying
>>>
>>>
>>>
>>> I've been playing around with the NC_004578.gbk (P.syringae DC3000
>>> chromosome) file I got from ncbi that I've been trying to
>>> display in a
>>>   biosql/gbrowse setup -- I got some of the data to
>>> partically display..
>>>
>>> I found that if I remove the whole genome sequence (ORIGIN record) at
>>> the end of NC_004578.gbk so that just the feature records remain, and
>>> load this into a fresh biosql db, CDS's display in GBrowse. But there
>>> are a couple of problems with what's displayed:
>>>
>>> 1) no features with a stop coordinate > 500,000 are shown, so
>>> for DC3000
>>> only about a 1/6 of the genome features are shown;
>>>
>>> 2) all the CDS features are duplicated.. there are two
>>> colored bars for
>>> each CDS. When you mouse over dulpicate bars they both
>>> display something
>>> like: "CDS: :813..1916". I thought this might have something
>>> to do with
>>> the fact that in the gbk file, most if not all of the CDS
>>> records have
>>> corresponding 'gene' records with the same exact coordinates, but the
>>> Genes have their own duplication problem... the gene records also
>>> display in duplicate ... mousing over the gene glyphs in the
>>> same region
>>> as the CDS above shows this: "Gene: :813..1916".
>>>
>>> Another test I performed with the NC_004578.gbk file is that
>>> I severely
>>> truncated the whole genome sequence at the end of the file.. removing
>>> all sequence after the '7141' line. And I removed all features in the
>>> file that had a coord > 7000. This left 4 CDSs and 4 genes. The file
>>> loads fine and displays all 4 features.. in duplicate. So
>>> when selecting
>>> the Landmark, "NC_004578:1..7200", all features are visible..
>>> 16 glyphs
>>> total due to duplication.
>>>
>>> The web log is not showing any errors of note..
>>>
>>> -Genevieve
>>>
>>>
>>>
>>> Lincoln Stein wrote:
>>>
>>>> Sounds like Simon and I will have to work through this.
>>> Probably the
>>>> display_name needs to get set more broadly.
>>>>
>>>> Lincoln
>>>>
>>>> On Friday 28 January 2005 07:30 pm, Hilmar Lapp wrote:
>>>>
>>>>> I haven't had a chance yet to look at this in the code so I am and
>>>>> probably sound a bit confused. In order to display something in
>>>>> gbrowse wouldn't you need coordinates?
>>>>>
>>>>> If what the code does is to fetch sequences, then they don't have
>>>>> coordinates - only their feature(s) do/does (which are
>>>>> auto-retrieved along with the seqs). This means that you'd have to
>>>>> have loaded the database with sequence entries whose feature table
>>>>> gives the coordinates of the *sequence*. Usually the feature table
>>>>> will give the coordinates of the features on the sequence, no?
>>>>> (unless it's a remote location)
>>>>>
>>>>> Assuming in your question you mean retrieving features by name, the
>>>>> naive answer is similar to how you do this for seq by accession,
>>>>> except you ask for the SeqFeatureI adaptor, provide a SeqFeatureI
>>>>> factory, specify SeqFeatureI in the collections, and constrain by
>>>>> the display_name property of the SeqFeatureI entity.
>>>>>
>>>>> However, this probably won't work for most dataload situations
>>>>> because bioperl doesn't set the display_name property in any of its
>>>>> rich format parsers. The corresponding column is optional in
>>>>> biosql, so there's no error or warning from that.
>>>>>
>>>>> So, if your name or identifier to search by is the value of a
>>>>> feature tag, technically it will be in the value column of the
>>>>> seqfeature_qualifier_value table unless you massaged the data
>>>>> structure prior to upload. You then need to set up a BioQuery with
>>>>> SeqFeatureI and Bio::Annotation::SimpleValue as entities to be
>>>>> joined, and constrain by value of the latter. This may mean nothing
>>>>> to most, but I hope Simon has some idea on what I'm talking about.
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Jan 28, 2005, at 12:14 PM, Lincoln Stein wrote:
>>>>>
>>>>>> There's a central call in the gbrowse/biosql adaptor called
>>>>>> get_feature_by_name() that calls
>>>>>> biosql->fetch_Seq_by_accession(). What it should do is to look
>>>>>> for seqfeatures if the
>>>>>> fetch_Seq_by_accession() doesn't return a result.
>>>>>>
>>>>>> This should be a simple fix .  Simon, HIlmar, what is the
>>>>>> appropriate biosql call to retrieve seqfeatures?
>>>>>>
>>>>>> Lincoln
>>>>>>
>>>>>> On Friday 28 January 2005 02:26 pm, Hilmar Lapp wrote:
>>>>>>
>>>>>>> So how do others do this then on biosql? Simon ran a benchmark
>>>>>>> that included biosql. Ah - that was on an artifical dataset,
>>>>>>> right? I thought Simon's been running gbrowse on top of biosql
>>>>>>> for some demo site on real data?
>>>>>>>
>>>>>>> So this may need more work then in that the bridging code should
>>>>>>> query either bioentry, or seqfeature, or possibly both, maybe
>>>>>>> configurable?
>>>>>>>
>>>>>>> 	-hilmar
>>>>>>>
>>>>>>> On Thursday, January 27, 2005, at 12:59  PM, Marc Logghe wrote:
>>>>>>>
>>>>>>>> Hi Genevieve,
>>>>>>>> my posts to gmod-gbrowse at lists.sourceforge.net seem to get lost
>>>>>>>> one way or another.
>>>>>>>>
>>>>>>>> Anyhow, I am afraid I will not be able to help you out ...
>>>>>>>> I can only make a few remarks.
>>>>>>>> As far as I understand your pseudomonas biosql database
>>>>>>>> contains 1 bioentry with the accession NC_004578 and sequence
>>>>>>>> length 6397126 bp. A query in the gbrowse/biosql combination
>>>>>>>> will only work for that accession and will return the complete
>>>>>>>> segment. So I guess you get a kind of timeout because the the
>>>>>>>> fetching of the bioentry from biosql takes too long.
>>>>>>>> Also, as far as I know, it is not possible to query for
>>>>>>>> features residing on that segment, e.g. the gene PSPTO0041.
>>>>>>>> That is because gbrowse/biosql will only look for the bioentry
>>>>>>>> in biosql with the accession number PSPTO0041 and not the gene
>>>>>>>> feature with that locus_tag !
>>>>>>>> This is probably not the behaviour you want.
>>>>>>>> An option I see, is that you convert the genbank record into
>>>>>>>> gff and load that in gbrowse/chado or gbrowse/gff.
>>>>>>>> I think genbank2gff3.pl is especially suited to do the
>>>>>>>> conversion. Hope I am not terribly wrong here ...
>>>>>>>>
>>>>>>>> Regards,
>>>>>>>> Marc
>>>>>>>>
>>>>>>>>
>>>>>>>>> -----Original Message-----
>>>>>>>>> From: Genevieve DeClerck [mailto:gad14 at cornell.edu]
>>>>>>>>> Sent: Thursday, January 27, 2005 6:14 PM
>>>>>>>>> To: Marc Logghe
>>>>>>>>> Cc: gmod-gbrowse at lists.sourceforge.net
>>>>>>>>> Subject: Re: [Gmod-gbrowse] features not displaying
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Right, thanks Marc - I lost that line when I created my conf
>>>>>>>>> file from
>>>>>>>>> scratch (from 06.biosql.conf) for the umpteenth time. With
>>>>>>>>> that line (and init_code.pl) I can successfully get the cds in
>>>>>>>>> the 'parkin' example biosql database to display! So I moved to
>>>>>>>>> the next step and created a new biosql db and loaded it with
>>>>>>>>> data that I'm more interested
>>>>>>>>> in.. the gbk file from ncbi of Pseudomonas syringae features
>>>>>>>>> (ftp://bio-mirror.net/biomirror/ncbigenomes/Bacteria/Pseudomon
>>>>>>>>> as_syringae/NC_004578.gbk).
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I seem to be encountering a similar problem as with the
>>>>>>>>> example parkin
>>>>>>>>> db previous to adding back that line - everything appears to
>>>>>>>>> be operating correctly in the browser, no errors in the web
>>>>>>>>> log, but no features appear for CDS's or anything else.
>>>>>>>>> Translation frames, GC content and sequence display fine.
>>>>>>>>>
>>>>>>>>> I'm starting to think that there's something amiss with how
>>>>>>>>> the NC_004578.gbk data is stored in the database... or
>>>>>>>>> something that biosql/gbrowse doesn't like about it. However,
>>>>>>>>> I do not see anything weird with the data when I browse
>>>>>>>>> through it in mysql. THe conf file i'm
>>>>>>>>> using for the NC_004578 db is pretty much the same as what I
>>>>>>>>> used for the parkin db.. just the appropriate changes in the
>>>>>>>>> db_args def.
>>>>>>>>>
>>>>>>>>> Any thoughts?
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Genevieve
>>>>>>>>>
>>>>>>>>> Marc Logghe wrote:
>>>>>>>>>
>>>>>>>>>> Hi Genevieve,
>>>>>>>>>> I am pretty sure it will be fixed when you adjust your conf
>>>>>>>>>
>>>>>>>>> like I suggested earlier.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> init_code    = do "$main::CONF_DIR/init_code.pl";
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> and put init_code.pl in your gbrowse.conf directory.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> *Bio::SeqFeature::Generic::attributes =
>>>>>>>>>
>>>>>>>>> \&Bio::SeqFeature::Generic::get_tag_values;
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> *Bio::SeqFeature::Generic::method =
>>>>>>>>>
>>>>>>>>> \&Bio::SeqFeature::Generic::primary_tag;
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> *Bio::SeqFeature::Generic::type = sub {
>>>>>>>>>>   my $feat = shift;
>>>>>>>>>>   my ($method) = $feat->primary_tag;
>>>>>>>>>>   my ($source) = $feat->source_tag;
>>>>>>>>>>   return $method;
>>>>>>>>>> };
>>>>>>>>>> *Bio::SeqFeature::Generic::name = sub {
>>>>>>>>>>   my $feat = shift;
>>>>>>>>>>   my $name = eval {($feat->get_tag_values('name'))[0]};
>>>>>>>>>>   $name ||= eval {($feat->get_tag_values('label'))[0]};
>>>>>>>>>>   $name ||= eval {($feat->get_tag_values('db_xref'))[0]};
>>>>>>>>>> #   $name ||= 'unknown';
>>>>>>>>>>   print STDERR "name = $name\n";
>>>>>>>>>>   return $name;
>>>>>>>>>> }
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> I tested it by commenting out the init_code line in my conf
>>>>>>>>>
>>>>>>>>> and I have the same things happening as you mention: no
>>>>>>>>> features show up, no errors in the log.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> ML
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> I can't for the life of me figure out why features/glyphs
>>>>>>>>>>> are not displaying in gbrowse. Everything else in the
>>>>>>>>>>> browser page is displaying
>>>>>>>>>>> fine - the header section, the footer, etc. A couple of
>>>>>>>>>>> things display
>>>>>>>>>>> ok in the feature window... GC Content, Translation fwd and
>>>>>>>>>>> rev (including DNA sequence when zoomed all the way down).
>>>>>>>>>>> But no real features, such as CDS, are displayed. The CDS
>>>>>>>>>>> track has a label, "CDS,"
>>>>>>>>>>> but the rest is just plain empty, where I know there should
>>>>>>>>>>> be a feature.
>>>>>>>>>>>
>>>>>>>>>>> I have gbrowse 1.62 running with a biosql-mysql database
>>>>>>>>>
>>>>>>>>> loaded with
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>> bioperl-db example data file 'parkin.gb', which has one CDS.
>>>>>>>>>>> [I just got
>>>>>>>>>>> this setup working yesterday, thanks to help from this list
>>>>>>>>>>> and BioSQL-l
>>>>>>>>>>> - see posts from jan 25 2005: "gbrowse on top of biosql"].
>>>>>>>>>>> There are no
>>>>>>>>>>> errors in the web error log or the mysql log. I triple
>>>>>>>>>>> checked that the
>>>>>>>>>>> parkin data is actually in the database and it is.
>>>>>>>>>>>
>>>>>>>>>>> ..I'm thinking there must be something wrong with my gbrowse
>>>>>>>>>>> conf file
>>>>>>>>>>> for this database.. in particular in the track section. But
>>>>>>>>>>> if that were
>>>>>>>>>>> the case, wouldn't I be seeing errors in my httpd error
>>>>>>>>>
>>>>>>>>> log? The conf
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>> file i have is almost an exact copy of a conf file that i've
>>>>>>>>>>> seen referred to in the docs: 06.biosql.conf. The track
>>>>>>>>>>> stanzas look reasonable, going from info in docs and
>>>>>>>>>>> tutorial. How do I debug the conf file??
>>>>>>>>>>> Or should I be looking somewhere else?
>>>>>>>>>>>
>>>>>>>>>>> My biosql.conf file is pasted below.
>>>>>>>>>>>
>>>>>>>>>>> Any clues much appreciated.
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Genevieve
>>>>>>>>>>>
>>>>>>>>>>> #************** biosql.conf *****************
>>>>>>>>>>>
>>>>>>>>>>> [GENERAL]
>>>>>>>>>>> description = biosql
>>>>>>>>>>> db_adaptor  = Bio::DB::Das::BioSQL
>>>>>>>>>>> db_args     = driver    mysql
>>>>>>>>>>> 	      dbname    biosql
>>>>>>>>>>> 	      namespace genbank
>>>>>>>>>>> 	      host      localhost
>>>>>>>>>>> 	      user      nobody
>>>>>>>>>>>              pass      ''
>>>>>>>>>>>
>>>>>>>>>>> plugins = SequenceDumper FastaDumper RestrictionAnnotator
>>>>>>>>>>>
>>>>>>>>>>> # Web site configuration info
>>>>>>>>>>> stylesheet  = /gbrowse/gbrowse.css
>>>>>>>>>>> buttons     = /gbrowse/images/buttons
>>>>>>>>>>> tmpimages   = /gbrowse/tmp
>>>>>>>>>>>
>>>>>>>>>>> # where to link to when user clicks in detaild view
>>>>>>>>>>> #link          =
>>>>>>>>>>> http://localhost/perl/gbrowse?ref=$ref;start=$start;stop=$en
>>>>>>>>>>> d link          = AUTO
>>>>>>>>>>>
>>>>>>>>>>> # what image widths to offer
>>>>>>>>>>> image widths  = 450 640 800 1024
>>>>>>>>>>>
>>>>>>>>>>> # default width of detailed view (pixels)
>>>>>>>>>>> default width = 800
>>>>>>>>>>> default features = CDS
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> # max and default segment sizes for detailed view
>>>>>>>>>>> max segment     = 500000
>>>>>>>>>>> default segment = 50000
>>>>>>>>>>>
>>>>>>>>>>> # zoom levels
>>>>>>>>>>> zoom levels    = 100 200 1000 2000 5000 10000 20000 40000
>>>>>>>>>>> 100000 200000
>>>>>>>>>>> 500000 1000000
>>>>>>>>>>> low res = 200000
>>>>>>>>>>>
>>>>>>>>>>> # colors of the overview, detailed map and key
>>>>>>>>>>> overview bgcolor = wheat
>>>>>>>>>>> detailed bgcolor = white
>>>>>>>>>>> key bgcolor      = beige
>>>>>>>>>>>
>>>>>>>>>>> footer = <hr>
>>>>>>>>>>> 	<table width="100%">
>>>>>>>>>>> 	<TR>
>>>>>>>>>>> 	<TD align="LEFT" class="databody">
>>>>>>>>>>> 	For the source code for this browser, see the <a
>>>>>>>>>>> href="http://www.gmod.org">
>>>>>>>>>>> 	Generic Model Organism Database Project.</a>  For other
>>>>>>>>>>> questions, send
>>>>>>>>>>> 	mail to <a
>>>>>>>>>>> href="mailto:lstein at cshl.org">lstein at cshl.org</a>. </TD>
>>>>>>>>>>> 	</TR>
>>>>>>>>>>> 	</table>
>>>>>>>>>>> 	<hr>
>>>>>>>>>>> 	<pre>$Id: 06.biosql.conf,v 1.1 2003/06/26 12:32:23
>>>>>>>>>>> lstein Exp $</pre>
>>>>>>>>>>>
>>>>>>>>>>> # examples to show in the introduction
>>>>>>>>>>> examples = AB019558
>>>>>>>>>>>
>>>>>>>>>>> # "automatic" classes to try when an unqualified identifier
>>>>>>>>>>> is given automatic classes = Accession
>>>>>>>>>>>
>>>>>>>>>>> [TRACK DEFAULTS]
>>>>>>>>>>> glyph       = generic
>>>>>>>>>>> height      = 8
>>>>>>>>>>> bgcolor     = cyan
>>>>>>>>>>> fgcolor     = cyan
>>>>>>>>>>> fontcolor   = black
>>>>>>>>>>> font2color  = blue
>>>>>>>>>>> label density = 25
>>>>>>>>>>> bump density  = 100
>>>>>>>>>>> description = 1
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ############################################################
>>>>>>>>>>> ## ##################
>>>>>>>>>>> # the remainder of the sections configure particular
>>>>>>>>>>> features to sho
>>>>>>>>>>> ############################################################
>>>>>>>>>>> ## ##################
>>>>>>>>>>>
>>>>>>>>>>> [CDS]
>>>>>>>>>>> feature      = CDS
>>>>>>>>>>> glyph        = transcript2
>>>>>>>>>>> #glyph        = generic
>>>>>>>>>>> bgcolor      = turquoise
>>>>>>>>>>> fgcolor      = black
>>>>>>>>>>> height       = 10
>>>>>>>>>>> connector    = solid
>>>>>>>>>>> key           = CDS
>>>>>>>>>>>
>>>>>>>>>>> [REPEAT]
>>>>>>>>>>> feature       = repeat_region
>>>>>>>>>>> glyph         = generic
>>>>>>>>>>> bgcolor       = red
>>>>>>>>>>> height        = 10
>>>>>>>>>>> description   = 1
>>>>>>>>>>> key           = Repeat regions
>>>>>>>>>>>
>>>>>>>>>>> [TranslationF]
>>>>>>>>>>> glyph        = translation
>>>>>>>>>>> global feature = 1
>>>>>>>>>>> frame0       = cadetblue
>>>>>>>>>>> frame1       = blue
>>>>>>>>>>> frame2       = darkblue
>>>>>>>>>>> height       = 20
>>>>>>>>>>> fgcolor      = purple
>>>>>>>>>>> strand       = +1
>>>>>>>>>>> translation  = 3frame
>>>>>>>>>>> key          = 3-frame translation (forward)
>>>>>>>>>>>
>>>>>>>>>>> [DNA/GC Content]
>>>>>>>>>>> glyph        = dna
>>>>>>>>>>> global feature = 1
>>>>>>>>>>> height       = 40
>>>>>>>>>>> do_gc        = 1
>>>>>>>>>>> fgcolor      = red
>>>>>>>>>>> axis_color   = blue
>>>>>>>>>>>
>>>>>>>>>>> [TranslationR]
>>>>>>>>>>> glyph        = translation
>>>>>>>>>>> global feature = 1
>>>>>>>>>>> frame0       = darkred
>>>>>>>>>>> frame1       = red
>>>>>>>>>>> frame2       = crimson
>>>>>>>>>>> height       = 20
>>>>>>>>>>> fgcolor      = blue
>>>>>>>>>>> strand       = -1
>>>>>>>>>>> translation  = 3frame
>>>>>>>>>>> key          = 3-frame translation (reverse)
>>>>>>>>>>>
>>>>>>>>>>> #****************************************************
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
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>>>>>>
>>>>>> --
>>>>>> Lincoln D. Stein
>>>>>> Cold Spring Harbor Laboratory
>>>>>> 1 Bungtown Road
>>>>>> Cold Spring Harbor, NY 11724
>>>>>>
>>>>>> NOTE: Please copy Sandra Michelsen <michelse at cshl.edu> on
>>>>>> all emails regarding scheduling and other time-critical topics.
>>>>
>>>>
>>>
>>>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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