Zoom.it is a free service for viewing and sharing high-resolution imagery. You give us the link to any image ( including SVG, pdfs) on the web along with a nice short URL.. As a test, I used the SVG file "Tree of life with genome size.svg" on wikipedia and here is the awesome result generated by Zoom.it:
I've just started creating a wikipedia infobox to annotate the biological databases in wikipedia. If many articles use this template, then it will be possible to parse the them and to create a list of the databases providing some web services, some SPARQL endpoints, having a download area etc...
The infobox itself is still a draft, so feel free to modify it or to suggest some other fields in the 'Talk' page.
Apache CXF is a Web Services framework. In this post, I'll will describe how I implemented a Web Service translating a DNA to a protein using the web server Apache Tomcat and the CXF libraries.
./translate/WEB-INF/classes/bio/TranslateImpl.javaThe service was compiled and deployed using the following Makefile:
./translate/WEB-INF/classes/bio/Translate.java
./translate/WEB-INF/beans.xml
./translate/WEB-INF/web.xml
Translate
| Endpoint address: http://localhost:8080/translate/translateMit WSDL : {http://bio/}TranslateService Target namespace: http://bio/ |
Translate
| Endpoint address: http://localhost:8080/translate/translateStd WSDL : {http://bio/}TranslateService Target namespace: http://bio/ |
I recently asked on Biostar if it would be worth to mask the non-genic sequence before aligning the short reads on the reference after an exome sequencing. Although I was convinced by the answer of lh3, I was curious to observe the difference with some real data.
I've downloaded two fastqs files from ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/data/NA20772/sequence_read/ERR004053_*.recal.fastq.gz and the sequence for the human chromosome chr1 from the UCSC.
One copy of chr1.fa was masked using the UCSC knownGene table +/- 10kb using a custom software. The bases were replaced by a 'N' if they were not contained in a genic region+/-10kb.
100005921 100005931 100005941 100005951 100005961 100005971
tgctaattggtcagattggagatggaatca*tggggggtcgacgtgaggttttcttgctgtcttct
....G.........G............... MM.......R.A....RK.................
.. ,,,,,,,,,,,,,,cac,,,,,,,,,a,,,,a,,, ,,,,,,,,,,,,,
.... ..........*CA.......A.A.......N....... ,,,,,,
.. ..........*CA.......A.A............... ,,,,
G...G..G.. ..........*CA.......A.A...............
....G.........G..T.. ...........T.................
....G....... .....A.....T.................
,,,,g,,,,,,,,,g,,,,,,,,,,,,,,,*,,,,, ..............G........
100005931 100005941 100005951 100005961 100005971 100005981in this case, it is visiblethat the reads have been more correctly aligned on the non-masked sequence.
tcagattggagatggaatcatggggggtcgacgtgaggttttcttgctgtcttctgttcctgggtg
..........CA.......R.A.....K............................
..........CA.......A.A.......N.......
...........T.........................
.....A.....T.........................
.A..................................
..............G...................
The Variant Call Format is a text file format generated by many tools for NGS. It contains meta-information lines, a header line, and then data lines describing how the mutations were called. I don't like this format because it cannot be used to store some hierachical annotations (like json or xml), nevertheless it is a de facto standard.
I wrote a tool called vcfannotator to append a set of annotations from the UCSC database to a VCF file. As I wanted to keep this tool simple and without any dependencies, it only uses the flat files available from the download area at the UCSC.
This tools appends several informations:
jsandbox/src/sandbox/VCFAnnotator.java.In my previous post , I used Node.js to translate a DNA to a protein on the Server-side, using javascript. In the following post, I again will translate a DNAn but this time by calling a specialized C program on the server side.
(wikipedia) Node.js is an evented I/O framework for the V8 JavaScript engine on Unix-like platforms. It is intended for writing scalable (javascript-based) network programs such as web servers.
In the following post I will create a javascript server translating a DNA to a protein.
Yesterday, Andrew Su asked on Biostar: "Given a gene, what is the best automated method to identify the world experts? ".
Here is my solution:
I recently asked on Biostar if it would be possible to align two sequences while displaying their respective annotations.
As both answers I received (SPICE and jalview ) require a graphical interface, I quickly wrote a command-line java program doing the job. This program reads a NCBI/BLAST XML output and, if the 'query' or the 'hit' definition lines start with "gi|....", it fetches the Genbank records and the annotations for the sequence and map them onto the alignments.
The program is available on github at https://github.com/lindenb/jsandbox/blob/master/src/sandbox/BlastAnnotation.java.
java -jar dist/blastannot.jar ~/jeter.blast.xml
QUERY: Homo sapiens eukaryotic translation initiation factor 4 gamma, 1 (EIF4G1), transcript variant 2, mRNA
ID:gi|303227906|ref|NM_198241.2| Len:5538
>Mus musculus eukaryotic translation initiation factor 4, gamma 1 (Eif4g1), transcript variant 2, mRNA
NM_001005331
id:gi|56699433|ref|NM_001005331.1| len:5460
e-value:0 gap:138 bitScore:6818.02
#####:############################################ exon 1..180 gene:EIF4G1
QUERY 000000053 GGCGCCGGCTGCGCCTGCGGAGAAGCGGTGGCCGCCGAGCGGGATCTGTG 000000102
||||| ||||||||||||||||||||||||||||||||||||||||||||
HIT 000000001 GGCGCTGGCTGCGCCTGCGGAGAAGCGGTGGCCGCCGAGCGGGATCTGTG 000000050
#####:############################################ exon 1..128 gene:Eif4g1
################################################## exon 1..180 gene:EIF4G1
QUERY 000000103 CGGGGAGCCGGAAATGGTTGTGGACTACGTCTGTGCGGCTGCGTGGGGCT 000000152
||||||||||||||||||||||||||||||||||||||||||||||||||
HIT 000000051 CGGGGAGCCGGAAATGGTTGTGGACTACGTCTGTGCGGCTGCGTGGGGCT 000000100
################################################## exon 1..128 gene:Eif4g1
############::::::::::###### exon 1..180 gene:EIF4G1
#:::::::::::::###::::: exon 181..237 gene:EIF4G1
QUERY 000000153 CGGCCGCGCGGACTGAAGGAGACTGAAGGCCCTCGGATGCCCAGAACCTG 000000202
|||||||||||| ||||||| |||
HIT 000000101 CGGCCGCGCGGA----------CTGAAGG-------------AGA----- 000000122
############----------#######-------------### gene 1..5460 gene:Eif4g1
############----------#######-------------### exon 1..128 gene:Eif4g1
::::::::::::::::::::::##:##:::::::# exon 181..237 gene:EIF4G1
############### exon 238..331 gene:EIF4G1
QUERY 000000203 TAGGCCGCACCGTGGACTTGTTCTTAATCGAGGGGGTGCTGGGGGGACCC 000000252
|| || ||||||||||||||||
HIT 000000123 ----------------------CTGAA-------GGTGCTGGGGGGACCC 000000143
----------------------##:##-------# exon 1..128 gene:Eif4g1
############### exon 129..222 gene:Eif4g1
#:###############################:###:############ exon 238..331 gene:EIF4G1
##############:###:############ CDS 272..5071 gene:EIF4G1
QUERY 000000253 TGATGTGGCACCAAATGAAATGAACAAAGCTCCACAGTCCACAGGCCCCC 000000302
| ||||||||||||||||||||||||||||||| ||| ||||||||||||
HIT 000000144 TAATGTGGCACCAAATGAAATGAACAAAGCTCCCCAGCCCACAGGCCCCC 000000193
#:###############################:###:############ exon 129..222 gene:Eif4g1
##############:###:############ CDS 163..4944 gene:Eif4g1
(...)
############:#:#:#####:######:#:########:##:###### exon 4890..5521 gene:EIF4G1
############:#:#:#####:######:#:########:##:###### STS 4948..5505 gene:EIF4G1
############:#:#:#####:######:#:########:##:###### STS 5174..5403 gene:EIF4G1
QUERY 000005319 TTGGTGTGTCTTGGGGTGGGGAGGGGCACCAACGCCTGCCCCTGGGGTCC 000005368
|||||||||||| | | ||||| |||||| | |||||||| || ||||||
HIT 000005201 TTGGTGTGTCTTTGCGGGGGGAAGGGCACTACCGCCTGCCTCTAGGGTCC 000005250
############:#:#:#####:######:#:########:##:###### exon 4760..5396 gene:Eif4g1
::##############:##########:###################### exon 4890..5521 gene:EIF4G1
::##############:##########:###################### STS 4948..5505 gene:EIF4G1
::##############:##########:####### STS 5174..5403 gene:EIF4G1
QUERY 000005369 TTTTTTTTATTTTCTGAAAATCACTCTCGGGACTGCCGTCCTCGCTGCTG 000005418
|||||||||||||| |||||||||| ||||||||||||||||||||||
HIT 000005251 --TTTTTTATTTTCTG-AAATCACTCTTGGGACTGCCGTCCTCGCTGCTG 000005297
--##############-##########:###################### exon 4760..5396 gene:Eif4g1
######################:#############:############# exon 4890..5521 gene:EIF4G1
######################:#############:############# STS 4948..5505 gene:EIF4G1
QUERY 000005419 GGGGCATATGCCCCAGCCCCTGTACCACCCCTGCTGTTGCCTGGGCAGGG 000005468
|||||||||||||||||||||| ||||||||||||| |||||||||||||
HIT 000005298 GGGGCATATGCCCCAGCCCCTGCACCACCCCTGCTGCTGCCTGGGCAGGG 000005347
######################:#############:############# exon 4760..5396 gene:Eif4g1
#:##-############################################: exon 4890..5521 gene:EIF4G1
#:##-################################# STS 4948..5505 gene:EIF4G1
###### polyA_signal 5496..5501 gene:EIF4G1
# polyA_site 5516 gene:EIF4G1
QUERY 000005469 GGAA-GGGGGGGCACGGTGCCTGTAATTATTAAACATGAATTCAATTAAG 000005517
| || ||||||||||||||||||||||||||||||||||||||||||||
HIT 000005348 GAAAGGGGGGGGCACGGTGCCTGTAATTATTAAACATGAATTCAATTAAA 000005397
#:##:############################################ exon 4760..5396 gene:Eif4g1
:::# exon 4890..5521 gene:EIF4G1
# polyA_site 5521 gene:EIF4G1
QUERY 000005518 CTCAAAAAAAAAAAAAAAAAA 000005538
||||||||||||||||||
HIT 000005398 AAAAAAAAAAAAAAAAAAAAA 000005418
