I have problem while trying to analyze data. The window will pop up and said " Could not run BLAST, please check it is installed, and BRIG's BLAST location is correct"I specify and install BLAST+ in the location as manual explain "C:\Program Files\NCBI\blast-2.10.0+\bin" but it is still pop up Could not run blast.Could you please help me about that?PS I use WINDOW, I install "ncbi-blast-2.10.0+-win64.exe"
Hi Panida Nobthai! Have you tried not specifying the location of BLAST i.e. leaving the BLAST binary folder option blank? When I ran BRIG in Windows, I usually don't have to specify the location of BLAST and it still works. In fact, I recall having issues when I do specify the location. Please keep me updated!
@@user-zv7wt8ke9y Hi! I played around with this and have identified the potential issue. One limitation of BRIG is that when you're specifying a path, there cannot be any spaces in any directories. For example, if you specified the bin folder as "C:\Program Files\NCBI\blast-2.10.0+\bin," BRIG is not able to recognize this because of the space between the words "Program" and "Files" in the folder "Program Files." To work around this, copy the BLAST bin folder to another location such as "C:\Users\User\Documents\" and specify the BLAST binary folder as "C:\Users\User\Documents\bin." Please let me know if this solves your issue!
This video is very helpful. I will be happy if you can share a video which shows, how to merge the annotated several scaffolds and make a complete genome.
Thanks Ajay Kumar Baranwal! Next, I'm planning to post a tutorial on using a different bioinformatics software called Geneious. It is capable of performing different types of analysis including genome assembly so stay tuned!
Hi Daren!!!, i add my files into the data pool as the first step, i select my output folder and then I click submit. There's an error that says that my query sequence folder contains a space that belongs to my user name. Any suggestions of what I can do with this? i tried using ""between my user name but it is still not working..
Hi jimmysantander! As far as I know, BRIG does not offer a high-throughput way to extract the gaps. It is more intended for specific inquiries such as "is gene X present in this set of genomes?" and "how different are these genomes overall?" If all the genomes you wanted to compare are in the MicroScope Microbial Genome Annotation & Analysis Platform database, I recommend using their comparative genomics tools to identify sequences that are part of pan-genomes. Good luck!
Hey Daren, I have troubles using BRIG when generating a comparison with a multi fasta. BRIG cant find my sequences, even for the reference bateria where i got my genes from. I dont know how to fix this problem.. Maybe someone can help!
Hello Daren, thank you for this tutorial it helped a lot but still I am not getting rings. Just one black ring in the centre although legends and everything is there but no ring. I am not sure if I am using the right file format. I have tried .gb and .fna as well but still no result. Can you please help?
Hi Daren, its nice video. I have successfully executed BRIG. But I have an issue with the image generated. The legends of the BRIG-generated figure is getting overlaid on the circular map and a part of the circle can not be visualized. Can you please give me a solution?
Hi Daren, thank you for your tutorial! I ran into a problem at the end of running BLAST and it came up with this message: Rendering CGVIEW image... java -Xmx1500m -jar cgview\cgview.jar -f jpg -i D:\Blasttest\scratch\Manila.gb.xml -o D:\Blasttest\blasttest.jpg Error occurred during initialization of VM Could not reserve enough space for 1536000KB object heap Was there a step that I had to fix before running it? I tried to use my 5TB harddrive to save it, but it still says it cannot save.
I encountered a similar issue. I found a solution at sourceforge.net/p/brig/support-requests/2/. On the screen right before you submit, access Preferences at the top left --> BRIG options --> Image settings and edit the 'Image render memory (MB)' field to 700 (or anything feasible under 1500).
Hello, I've tried adding my query sequences, however it does not seem to detect my sequence files. I've noticed your sequences are in the .gbk format while my sequences are in the .gff format. Could it be that, or would you happen to know any fixes for my sequences not showing up when i click the 'add to data pool' button?
Thanks for your good tutorial want to use BLAST Ring Image Generator (BRIG) locally, but before that I need to run Blast + with C++ so , I faced with some problem to use code? Do you have any ready code to install blast + or do you have any recommendations to run blast +? Why installed of blast + is so difficult I am not programmer so I faced with really problems 😢
Hi Maryam Beiranvand ! Check out 1:57 of the video to find the link where you can download and install BLAST. If this hasn't worked for you, would you mind explaining what specific issues you're running into?
I have a question. After running BRIG the image is generated and also a folder named "scratch" with two huge files with the extension .ndb and .ntf Is there any way that i can limit these files size?
Hi Karla! Limiting these files was not discussed in the manual. There are likely other ways to do it but I am unfamiliar. If you figure it out, please let me know. Good luck!
This is the best tutorial for BRIGS I have come across, I did everything step by step and got a lovely graph. the only thing is that at the end the program told me that it couldn't add the "legend was removed because it is too large for the canvas." what can I do to overcome this problem and have my legends added?
Hi Idalio Amaranto ! BRIG is meant for comparing prokaryotic genomes. I can see it potentially working with eukaryotes but it will likely require you to process the genomes beforehand to get just the coding regions of the genome. Good luck and please let me know if you find another useful tool for your purposes!
Hi! If you're downloading the genome from NCBI, you can select to obtain the genbank instead of the fasta format. While I have not used them recently, there are also direct tools you can use to convert your genome file from fasta to genbank. One tool you can try is EMBOSS seqret (www.ebi.ac.uk/Tools/sfc/emboss_seqret/). Good luck!
Thank you so much for the video. I ran it and it gives me error a legend was removed because it is too large for the canvas). How to modify the image setting to avoid this problem. Thank you.
Hi Walaa hussein ! At the starting window, you can go to "Preferences" and choose "Image Options." Here, you can play around with the height and width of your canvas as well as other settings to make sure your legend stays in. Good luck!
Hello Daren, I followed your instructions and I click on add to pool button of the BRIG, I got error massage as "file/ directory does not exist" . I tried multiple times but got the same error , could you help me please?
Hi Sai Prashanthi G! As long as they are in an accepted format like fasta, you should be able to use scaffolds as input! Good luck and please let me know how it goes!
I am facing problem in creating the image. I have followed all the instructions but the image that is produced shows only one ring instead of 14 rings. And in the brig window its showing database error and not enough space on disk. Thiugh i know there is enough space in disk. The download location for both blast and brig is desktop. Please help
Hi Sharmi! Here are a couple of suggestions copied from two previous comments: From Samuel Greenrod: Solution is at the bottom of this page: www.biostars.org/p/413294/ You need to make a new environment variable called "BLASTDB_LMDB_MAP_SIZE" with value "1000000". Instructions on how to do this are here: www.ncbi.nlm.nih.gov/books/NBK52637/ From Ray Shyone: The problem is that normally the Java virtual machine artificially limits the amount of memory. What worked for me is: Create a shortcut to the BRIG.jar JAR file. Edit the properties of the shortcut and add "java -mx2g -jar" to the start of the "Target:" field. -mx2g sets the maximum memory Java will allocate to BRIG. Run BRIG from the shortcut will solve this problem. I also recommend checking out Artemis Comparison Tool (ACT)! Good luck!
also, the folders where we have the genomes cant contain spaces right? every time that i try to upload some files, it says it contains an invalid name or space
I have a problem where in my case i am having more than 200 genomic sequences to be compared with my reference sequence. The resultant image which i obtained is showing only the GC Content and GC Skew rings, but not the rest of the remaning rings that corresponds to each genomic sequence which i have added to the data pool, in other words , only the two rings appeared on the image and the rest is blank,please help!! Note : I am having the updated version of Java and blast+ and blast legacy also are installed .
Hi Daniel Pyngrope! To more effectively help you, I have two follow-up questions. First, does it work if you only use a small number of genomes (less than 20)? Second, what version of Java are you using? BRIG is written in Java 1.6 and researchers have run into issues with BRIG with newer versions of Java. Check 1:15 of the video if you need help installing Java 1.6.
Hello Daren, Thank you for this very helpful video. I am having trouble running BRIG and I keep running into this problem: BLAST Database creation error: mdb_env_open: There is not enough space on the disk. I think I have enough storage space on my PC. Do you know how to fix this problem? Thank you.
Hi Ray Shyone, I have not encountered that issue before. I would probably play around with the location of your output folder to see if that solves the issue. If you figure out the problem, please let me know how!
Solution is at the bottom of this page: www.biostars.org/p/413294/ You need to make a new environment variable called "BLASTDB_LMDB_MAP_SIZE" with value "1000000". Instructions on how to do this are here: www.ncbi.nlm.nih.gov/books/NBK52637/
@@samuelgreenrod1812 Thanks for your reply! The problem is that normally the Java virtual machine artificially limits the amount of memory. What worked for me is: Create a shortcut to the BRIG.jar JAR file. Edit the properties of the shortcut and add "java -mx2g -jar" to the start of the "Target:" field. -mx2g sets the maximum memory Java will allocate to BRIG. Run BRIG from the shortcut will solve this problem. I also recommend checking out Artemis Comparison Tool (ACT)!
Hello thanks you for your good tutorial ,I have installed this program on windows 7 so I follow step by step based on manual book after finish running my picture is not complete. must I alignment my whole genome by bio edit software and than apply my whole genome on this software? Thanks for your help
Hi Maryam! In most cases, you don't need to process your genomes prior to using them with BRIG. What image do you get after running the program? Have you tried using other genomes or other formats (gbk, fasta, etc.) for the reference/query?
Hi @@rozgol2706! Based on your description, it seems like either your reference or query genome is not appearing in the output. One thing to try is to use a different genome file format which sometimes helps. If you share your email here, I'd be happy to correspond with you further and take a look at your image.
Hi nidhi vijayan ! I looked through the manual and played around with the image settings and I can only get 96 dpi. You might want to just save the file in a different format and use an image editing software to change the resolution to 300 dpi. If you find a way to do it using the software, please let me know!
Hi shawnfunstuff! BRIG isn't able to do that, unfortunately. I've used MicroScope Microbial Genome Annotation & Analysis Platform before but that would require that the genomes you're comparing are already uploaded in their database.
@@DarenGinete Thanks. I have seen BRIG images where they label the location and gene name of genomic islands, so there is some way to somehow use the brig image and track gene location. Apparently Mauve is better for genome comparisons and providing the absent/prensent gene lists.
@@DarenGinete Well there does appear to be a way to label gene IDs on these maps. I found out how to add every gene label, but not how to add only those genes that are missing from one strain, for example.
@@shawnfunstuff Yes, you are able to do that with BRIG. As far as I know, it doesn't have the capability to do the latter directly. It seems like it really is just meant to visualize genomic differences and other tools would be better suited for that type of analysis. If you're able to figure out a way to do so, however, please let me know!
hi,can you tell me why there are so many errors,and i can not create a picture Your query File: C:\Users\YJKJ\Desktop\新建文件夹\C2343.gb -------------------------------------- Formatting nucleotide file... Initializing XML output.. Running BLAST... Sequence length: 0 Formatting nucleotide file... makeblastdb -dbtype nucl -in E:\临时文档\2019年分析\scratch\C2343.gb.fna BLAST options error: E:\临时文档\2019年分析\scratch\C2343.gb.fna does not match input format type, default input type is FASTA blastn -outfmt 6 -query E:\临时文档\2019年分析\scratch\C2343.gb.fna -db E:\临时文档\2019年分析\scratch\C2343.gb.fna -out E:\临时文档\2019年分析\scratch\C2343.gb.fnaVsC2343.gb.fna.tab -task blastn BLAST Database error: No alias or index file found for nucleotide database [E:\临时文档\2019年分析\scratch\C2343.gb.fna] in search path [D:\Users\YJKJ\Downloads\BRIG-0.95-dist\BRIG-0.95-dist;;] Formatting nucleotide file... makeblastdb -dbtype nucl -in E:\临时文档\2019年分析\scratch\C2343.gb.fna BLAST options error: E:\临时文档\2019年分析\scratch\C2343.gb.fna does not match input format type, default input type is FASTA blastn -outfmt 6 -query E:\临时文档\2019年分析\scratch\C2315Chrome.gb.fna -db E:\临时文档\2019年分析\scratch\C2343.gb.fna -out E:\临时文档\2019年分析\scratch\C2315Chrome.gb.fnaVsC2343.gb.fna.tab -task blastn BLAST Database error: No alias or index file found for nucleotide database [E:\临时文档\2019年分析\scratch\C2343.gb.fna] in search path [D:\Users\YJKJ\Downloads\BRIG-0.95-dist\BRIG-0.95-dist;;] Formatting nucleotide file... makeblastdb -dbtype nucl -in E:\临时文档\2019年分析\scratch\C2343.gb.fna BLAST options error: E:\临时文档\2019年分析\scratch\C2343.gb.fna does not match input format type, default input type is FASTA blastn -outfmt 6 -query E:\临时文档\2019年分析\scratch\pC2315-KPC.gb.fna -db E:\临时文档\2019年分析\scratch\C2343.gb.fna -out E:\临时文档\2019年分析\scratch\pC2315-KPC.gb.fnaVsC2343.gb.fna.tab -task blastn BLAST Database error: No alias or index file found for nucleotide database [E:\临时文档\2019年分析\scratch\C2343.gb.fna] in search path [D:\Users\YJKJ\Downloads\BRIG-0.95-dist\BRIG-0.95-dist;;] Formatting nucleotide file... makeblastdb -dbtype nucl -in E:\临时文档\2019年分析\scratch\C2343.gb.fna BLAST options error: E:\临时文档\2019年分析\scratch\C2343.gb.fna does not match input format type, default input type is FASTA blastn -outfmt 6 -query E:\临时文档\2019年分析\scratch\pC2343-4-KPC.gb.fna -db E:\临时文档\2019年分析\scratch\C2343.gb.fna -out E:\临时文档\2019年分析\scratch\pC2343-4-KPC.gb.fnaVsC2343.gb.fna.tab -task blastn BLAST Database error: No alias or index file found for nucleotide database [E:\临时文档\2019年分析\scratch\C2343.gb.fna] in search path [D:\Users\YJKJ\Downloads\BRIG-0.95-dist\BRIG-0.95-dist;;] Parsing BLAST Results... Rendering CGVIEW image... java -Xmx1500m -jar cgview\cgview.jar -f jpg -i E:\临时文档\2019年分析\scratch\C2343.gb.xml -o E:\临时文档\2019年分析\C2343.gb.jpg Parsing XML input. SYS_ERROR:org.xml.sax.SAXException: value for 'sequenceLength' attribute in cgview element must be greater than 10 in null at line 1 column 1046 SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.handleCgview(CgviewFactory.java:601) SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.startElement(CgviewFactory.java:510) SYS_ERROR: at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) SYS_ERROR: at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) SYS_ERROR: at org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source) SYS_ERROR: at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) SYS_ERROR: at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) SYS_ERROR: at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) SYS_ERROR: at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source) SYS_ERROR: at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) SYS_ERROR: at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.createCgviewFromFile(CgviewFactory.java:300) SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewIO.main(CgviewIO.java:1056) SYS_ERROR:The following error occurred: org.xml.sax.SAXException: value for 'sequenceLength' attribute in cgview element must be greater than 10 in null at line 1 column 1046 Done. thank you very much!!!
Hi! As you suggested in your follow up comment, your current sequence files might not be compatible with how BRIG is processing your data. I recommend trying different versions of your sequence files to see which ones work.
Hi Edson! You would have to restart the run again but if you use the same output folder, the program will recognize the files from the previous run and continue from there.
@@caseyhugheslago8850 concatenate your contig into single contig. Then u can use either fasta or fna file extension. if you have multiple contig than it will not work
